diff --git a/.github/issue_template.md b/.github/issue_template.md index 79269c9e..3d7e716c 100644 --- a/.github/issue_template.md +++ b/.github/issue_template.md @@ -1,12 +1,12 @@ ### Description of the issue: -*Try to be as clear as possible, e.g.: + #### Reproducing this issue: -*If applicable, please attach the problematic code. PLEASE DELETE THIS LINE.* + ```matlab INSERT CODE HERE ``` @@ -17,8 +17,7 @@ INSERT CODE HERE 2. Operating system (Windows/Mac/Linux; include version) **I hereby confirm that I have:** + - [ ] Followed the [guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/Installation) to install RAVEN. - [ ] Checked that a similar issue does not [already exist](https://github.com/SysBioChalmers/RAVEN/issues?utf8=%E2%9C%93&q=is%3Aissue) - [ ] If suitable, needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about the issue - -*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md index a114340e..ce928797 100644 --- a/.github/pull_request_template.md +++ b/.github/pull_request_template.md @@ -1,14 +1,12 @@ ### Main improvements in this PR: -*Pointwise mention what changes were made in what function. Examples: + **I hereby confirm that I have:** + - [ ] Tested my code on my own machine - [ ] Followed the [development guidelines](https://github.com/SysBioChalmers/RAVEN/wiki/DevGuidelines). - [ ] Selected `devel` as a target branch - [ ] If needed, asked first in the [Gitter chat room](https://gitter.im/SysBioChalmers/RAVEN) about this PR - -*Note: replace [ ] with [X] to check the box. PLEASE DELETE THIS LINE* diff --git a/.github/workflows/testing-comment.md b/.github/workflows/testing-comment.md new file mode 100644 index 00000000..c0c38f90 --- /dev/null +++ b/.github/workflows/testing-comment.md @@ -0,0 +1,7 @@ +This PR has been [automatically tested with GH Actions](https://github.com/SysBioChalmers/RAVEN/actions/runs/{GH_ACTION_RUN}). Here is the output of the tests: + +``` +{TEST_RESULTS} +``` + +> _Note: In the case of multiple test runs, this post will be edited._ \ No newline at end of file diff --git a/.github/workflows/testing.yml b/.github/workflows/testing.yml new file mode 100644 index 00000000..888c2aba --- /dev/null +++ b/.github/workflows/testing.yml @@ -0,0 +1,28 @@ +name: Testing + +on: [pull_request] + +jobs: + matlab-tests: + runs-on: self-hosted + + steps: + + - name: Checkout + uses: actions/checkout@v2 + + - name: Run tests + id: matlab-test + run: | + TEST_RESULTS=$(/usr/local/bin/matlab -nodisplay -nosplash -nodesktop -r "addpath(genpath('.')); cd('testing/unit_tests'); runtests(struct2table(dir('*.m')).name); exit;") + PARSED_RESULTS=$(echo $TEST_RESULTS | awk -F'.com.' '{ n = split($2, v, "__________"); for (i = 0; ++i <= n;) { print v[i] } }') + echo ::set-output name=results::$PARSED_RESULTS + + - name: Post comment + uses: NejcZdovc/comment-pr@v1 + with: + file: "testing-comment.md" + env: + GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}} + TEST_RESULTS: ${{steps.matlab-test.outputs.results}} + GH_ACTION_RUN: ${{github.run_id}} \ No newline at end of file diff --git a/core/checkModelStruct.m b/core/checkModelStruct.m index fd20ab87..381278ae 100755 --- a/core/checkModelStruct.m +++ b/core/checkModelStruct.m @@ -246,6 +246,18 @@ function checkModelStruct(model,throwErrors,trimWarnings) EM='The following reactions have bounds contradicting their reversibility:'; dispEM(EM,throwErrors,model.rxns(model.lb<0 & model.rev==0),trimWarnings); +%Multiple or no objective functions not allowed in SBML L3V1 FBCv2 +if numel(find(model.c))>1 + EM='Multiple objective functions found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance:'; + dispEM(EM,false,model.rxns(find(model.c)),trimWarnings); +elseif ~any(model.c) + EM='No objective function found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance'; + dispEM(EM,false); +end + +EM='The following reactions have contradicting bounds:'; +dispEM(EM,throwErrors,model.rxns(model.lb>model.ub),trimWarnings); + %Mapping of compartments if isfield(model,'compOutside') EM='The following compartments are in "compOutside" but not in "comps":'; diff --git a/core/compareModels.m b/core/compareRxnsGenesMetsComps.m old mode 100755 new mode 100644 similarity index 97% rename from core/compareModels.m rename to core/compareRxnsGenesMetsComps.m index 7af16a6d..37d1f9e7 --- a/core/compareModels.m +++ b/core/compareRxnsGenesMetsComps.m @@ -1,5 +1,5 @@ -function compStruct=compareModels(models,printResults) -% compareModels +function compStruct=compareRxnsGenesMetsComps(models,printResults) +% compareRxnsGenesMetsComps % Compares two or more models with respect to overlap in terms of genes, % reactions, metabolites and compartments. % @@ -23,7 +23,7 @@ % nElements vector with the number of elements for each % comparison % -% Usage: compStruct=compareModels(models,printResults) +% Usage: compStruct=compareRxnsGenesMetsComps(models,printResults) if nargin<2 printResults=true; diff --git a/core/convertToIrrev.m b/core/convertToIrrev.m index ecac9d0b..aae1e62f 100755 --- a/core/convertToIrrev.m +++ b/core/convertToIrrev.m @@ -14,13 +14,13 @@ % Usage: irrevModel=convertToIrrev(model,rxns) if nargin<2 - rxns=model.rxns; + I=true(numel(model.rxns),1); +else + I=getIndexes(model,rxns,'rxns',true); end irrevModel=model; -I=getIndexes(model,rxns,'rxns',true); - revIndexesBool=model.rev~=0 & I; revIndexes=find(revIndexesBool); if any(revIndexesBool) diff --git a/core/dispEM.m b/core/dispEM.m index 325ba758..9947f76f 100755 --- a/core/dispEM.m +++ b/core/dispEM.m @@ -42,6 +42,8 @@ function dispEM(string,throwErrors,toList,trimWarnings) end end if throwErrors==false + %Escape special characters, required for fprintf + errorText=regexprep(errorText,'(\\|\%|'')','\\$0'); fprintf([errorText '\n']); else throw(MException('',errorText)); diff --git a/core/permuteModel.m b/core/permuteModel.m index 15765f83..23a06cea 100755 --- a/core/permuteModel.m +++ b/core/permuteModel.m @@ -2,111 +2,155 @@ % permuteModel % Changes the order of the reactions or metabolites in a model % +% Input: % model a model structure -% indexes a vector with the same length as the number of reactions in the -% model which gives the new order of reactions -% type 'rxns' for reactions and 'mets' for metabolites +% indexes a vector with the same length as the number of items in the +% model, which gives the new order of items +% type 'rxns' for reactions, 'mets' for metabolites, 'genes' for +% genes, 'comps' for compartments % -% newModel an updated model structure +% Output: +% newModel an updated model structure % % Usage: newModel=permuteModel(model, indexes, type) newModel=model; indexes=indexes(:); -if strcmp(type,'rxns') - if isfield(newModel,'rxns') - newModel.rxns=newModel.rxns(indexes); - end - if isfield(newModel,'lb') - newModel.lb=newModel.lb(indexes); - end - if isfield(newModel,'ub') - newModel.ub=newModel.ub(indexes); - end - if isfield(newModel,'rev') - newModel.rev=newModel.rev(indexes); - end - if isfield(newModel,'c') - newModel.c=newModel.c(indexes); - end - if isfield(newModel,'S') - newModel.S=newModel.S(:,indexes); - end - if isfield(newModel,'rxnNames') - newModel.rxnNames=newModel.rxnNames(indexes); - end - if isfield(newModel,'rxnGeneMat') - newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); - end - if isfield(newModel,'grRules') - newModel.grRules=newModel.grRules(indexes); - end - if isfield(newModel,'subSystems') - newModel.subSystems=newModel.subSystems(indexes); - end - if isfield(newModel,'eccodes') - newModel.eccodes=newModel.eccodes(indexes); - end - if isfield(newModel,'equations') - newModel.equations=newModel.equations(indexes); - end - if isfield(newModel,'rxnMiriams') - newModel.rxnMiriams=newModel.rxnMiriams(indexes); - end - if isfield(newModel,'rxnComps') - newModel.rxnComps=newModel.rxnComps(indexes); - end - if isfield(newModel,'rxnFrom') - newModel.rxnFrom=newModel.rxnFrom(indexes); - end - if isfield(newModel,'rxnScores') - newModel.rxnScores=newModel.rxnScores(indexes); - end - if isfield(newModel,'rxnNotes') - newModel.rxnNotes=newModel.rxnNotes(indexes); - end - if isfield(newModel,'rxnReferences') - newModel.rxnReferences=newModel.rxnReferences(indexes); - end - if isfield(newModel,'rxnConfidenceScores') - newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); - end -end - -if strcmp(type,'mets') - if isfield(newModel,'mets') - newModel.mets=newModel.mets(indexes); - end - if isfield(newModel,'metNames') - newModel.metNames=newModel.metNames(indexes); - end - if isfield(newModel,'b') - newModel.b=newModel.b(indexes,:); - end - if isfield(newModel,'metComps') - newModel.metComps=newModel.metComps(indexes); - end - if isfield(newModel,'S') - newModel.S=newModel.S(indexes,:); - end - if isfield(newModel,'unconstrained') - newModel.unconstrained=newModel.unconstrained(indexes); - end - if isfield(newModel,'metMiriams') - newModel.metMiriams=newModel.metMiriams(indexes,:); - end - if isfield(newModel,'inchis') - newModel.inchis=newModel.inchis(indexes); - end - if isfield(newModel,'metFormulas') - newModel.metFormulas=newModel.metFormulas(indexes); - end - if isfield(newModel,'metFrom') - newModel.metFrom=newModel.metFrom(indexes); - end - if isfield(newModel,'metCharges') - newModel.metCharges=newModel.metCharges(indexes); - end +switch type + case 'rxns' + if isfield(newModel,'rxns') + newModel.rxns=newModel.rxns(indexes); + end + if isfield(newModel,'lb') + newModel.lb=newModel.lb(indexes); + end + if isfield(newModel,'ub') + newModel.ub=newModel.ub(indexes); + end + if isfield(newModel,'rev') + newModel.rev=newModel.rev(indexes); + end + if isfield(newModel,'c') + newModel.c=newModel.c(indexes); + end + if isfield(newModel,'S') + newModel.S=newModel.S(:,indexes); + end + if isfield(newModel,'rxnNames') + newModel.rxnNames=newModel.rxnNames(indexes); + end + if isfield(newModel,'rxnGeneMat') + newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); + end + if isfield(newModel,'grRules') + newModel.grRules=newModel.grRules(indexes); + end + if isfield(newModel,'subSystems') + newModel.subSystems=newModel.subSystems(indexes); + end + if isfield(newModel,'eccodes') + newModel.eccodes=newModel.eccodes(indexes); + end + if isfield(newModel,'equations') + newModel.equations=newModel.equations(indexes); + end + if isfield(newModel,'rxnMiriams') + newModel.rxnMiriams=newModel.rxnMiriams(indexes); + end + if isfield(newModel,'rxnComps') + newModel.rxnComps=newModel.rxnComps(indexes); + end + if isfield(newModel,'rxnFrom') + newModel.rxnFrom=newModel.rxnFrom(indexes); + end + if isfield(newModel,'rxnScores') + newModel.rxnScores=newModel.rxnScores(indexes); + end + if isfield(newModel,'rxnNotes') + newModel.rxnNotes=newModel.rxnNotes(indexes); + end + if isfield(newModel,'rxnReferences') + newModel.rxnReferences=newModel.rxnReferences(indexes); + end + if isfield(newModel,'rxnConfidenceScores') + newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); + end + case 'mets' + if isfield(newModel,'mets') + newModel.mets=newModel.mets(indexes); + end + if isfield(newModel,'metNames') + newModel.metNames=newModel.metNames(indexes); + end + if isfield(newModel,'b') + newModel.b=newModel.b(indexes,:); + end + if isfield(newModel,'metComps') + newModel.metComps=newModel.metComps(indexes); + end + if isfield(newModel,'S') + newModel.S=newModel.S(indexes,:); + end + if isfield(newModel,'unconstrained') + newModel.unconstrained=newModel.unconstrained(indexes); + end + if isfield(newModel,'metMiriams') + newModel.metMiriams=newModel.metMiriams(indexes,:); + end + if isfield(newModel,'inchis') + newModel.inchis=newModel.inchis(indexes); + end + if isfield(newModel,'metFormulas') + newModel.metFormulas=newModel.metFormulas(indexes); + end + if isfield(newModel,'metFrom') + newModel.metFrom=newModel.metFrom(indexes); + end + if isfield(newModel,'metCharges') + newModel.metCharges=newModel.metCharges(indexes); + end + case 'genes' + if isfield(newModel,'genes') + newModel.genes=newModel.genes(indexes); + end + if isfield(newModel,'geneComps') + newModel.geneComps=newModel.geneComps(indexes); + end + if isfield(newModel,'geneMiriams') + newModel.geneMiriams=newModel.geneMiriams(indexes); + end + if isfield(newModel,'geneShortNames') + newModel.geneShortNames=newModel.geneShortNames(indexes); + end + if isfield(newModel,'rxnGeneMat') + newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes); + end + case 'comps' + if isfield(newModel,'comps') + newModel.comps=newModel.comps(indexes); + end + if isfield(newModel,'compNames') + newModel.compNames=newModel.compNames(indexes); + end + if isfield(newModel,'compOutside') + newModel.compOutside=newModel.compOutside(indexes); + end + if isfield(newModel,'compMiriams') + newModel.compMiriams=newModel.compMiriams(indexes); + end + [~,J]=sort(indexes); % The *index* of compartment is used in next fields + if isfield(newModel,'metComps') + [toreplace, bywhat] = ismember(newModel.metComps,1:length(J)); + newModel.metComps(toreplace) = J(bywhat(toreplace)); + end + if isfield(model,'rxnComps') + [toreplace, bywhat] = ismember(model.rxnComps,1:length(J)); + model.rxnComps(toreplace) = J(bywhat(toreplace)); + end + if isfield(model,'geneComps') + [toreplace, bywhat] = ismember(model.geneComps,1:length(J)); + model.geneComps(toreplace) = J(bywhat(toreplace)); + end end end diff --git a/doc/core/checkModelStruct.html b/doc/core/checkModelStruct.html index 90aa5bf6..92e3e48f 100644 --- a/doc/core/checkModelStruct.html +++ b/doc/core/checkModelStruct.html @@ -305,116 +305,128 @@

SOURCE CODE ^'The following reactions have bounds contradicting their reversibility:'; 0247 dispEM(EM,throwErrors,model.rxns(model.lb<0 & model.rev==0),trimWarnings); 0248 -0249 %Mapping of compartments -0250 if isfield(model,'compOutside') -0251 EM='The following compartments are in "compOutside" but not in "comps":'; -0252 dispEM(EM,throwErrors,setdiff(model.compOutside,[{''};model.comps]),trimWarnings); -0253 end -0254 -0255 %Met names which start with number -0256 I=false(numel(model.metNames),1); -0257 for i=1:numel(model.metNames) -0258 index=strfind(model.metNames{i},' '); -0259 if any(index) -0260 if any(str2double(model.metNames{i}(1:index(1)-1))) -0261 I(i)=true; -0262 end -0263 end -0264 end -0265 EM='The following metabolite names begin with a number directly followed by space:'; -0266 dispEM(EM,throwErrors,model.mets(I),trimWarnings); -0267 -0268 %Non-parseable composition -0269 if isfield(model,'metFormulas') -0270 [~, ~, exitFlag]=parseFormulas(model.metFormulas,true,false); -0271 EM='The composition for the following metabolites could not be parsed:'; -0272 dispEM(EM,false,model.mets(exitFlag==-1),trimWarnings); -0273 end -0274 -0275 %Check if there are metabolites with different names but the same MIRIAM -0276 %codes -0277 if isfield(model,'metMiriams') -0278 miriams=containers.Map(); -0279 for i=1:numel(model.mets) -0280 if ~isempty(model.metMiriams{i}) -0281 %Loop through and add for each miriam -0282 for j=1:numel(model.metMiriams{i}.name) -0283 %Get existing metabolite indexes -0284 current=strcat(model.metMiriams{i}.name{j},'/',model.metMiriams{i}.value{j}); -0285 if isKey(miriams,current) -0286 existing=miriams(current); -0287 else -0288 existing=[]; -0289 end -0290 miriams(current)=[existing;i]; -0291 end -0292 end -0293 end -0294 -0295 %Get all keys -0296 allMiriams=keys(miriams); -0297 -0298 hasMultiple=false(numel(allMiriams),1); -0299 for i=1:numel(allMiriams) -0300 if numel(miriams(allMiriams{i}))>1 -0301 %Check if they all have the same name -0302 if numel(unique(model.metNames(miriams(allMiriams{i}))))>1 -0303 if ~regexp(allMiriams{i},'^sbo\/SBO:') % SBO terms are expected to be multiple -0304 hasMultiple(i)=true; -0305 end -0306 end -0307 end -0308 end +0249 %Multiple or no objective functions not allowed in SBML L3V1 FBCv2 +0250 if numel(find(model.c))>1 +0251 EM='Multiple objective functions found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance:'; +0252 dispEM(EM,false,model.rxns(find(model.c)),trimWarnings); +0253 elseif ~any(model.c) +0254 EM='No objective function found. This might be intended, but exportModel will fail due to SBML FBCv2 non-compliance'; +0255 dispEM(EM,false); +0256 end +0257 +0258 EM='The following reactions have contradicting bounds:'; +0259 dispEM(EM,throwErrors,model.rxns(model.lb>model.ub),trimWarnings); +0260 +0261 %Mapping of compartments +0262 if isfield(model,'compOutside') +0263 EM='The following compartments are in "compOutside" but not in "comps":'; +0264 dispEM(EM,throwErrors,setdiff(model.compOutside,[{''};model.comps]),trimWarnings); +0265 end +0266 +0267 %Met names which start with number +0268 I=false(numel(model.metNames),1); +0269 for i=1:numel(model.metNames) +0270 index=strfind(model.metNames{i},' '); +0271 if any(index) +0272 if any(str2double(model.metNames{i}(1:index(1)-1))) +0273 I(i)=true; +0274 end +0275 end +0276 end +0277 EM='The following metabolite names begin with a number directly followed by space:'; +0278 dispEM(EM,throwErrors,model.mets(I),trimWarnings); +0279 +0280 %Non-parseable composition +0281 if isfield(model,'metFormulas') +0282 [~, ~, exitFlag]=parseFormulas(model.metFormulas,true,false); +0283 EM='The composition for the following metabolites could not be parsed:'; +0284 dispEM(EM,false,model.mets(exitFlag==-1),trimWarnings); +0285 end +0286 +0287 %Check if there are metabolites with different names but the same MIRIAM +0288 %codes +0289 if isfield(model,'metMiriams') +0290 miriams=containers.Map(); +0291 for i=1:numel(model.mets) +0292 if ~isempty(model.metMiriams{i}) +0293 %Loop through and add for each miriam +0294 for j=1:numel(model.metMiriams{i}.name) +0295 %Get existing metabolite indexes +0296 current=strcat(model.metMiriams{i}.name{j},'/',model.metMiriams{i}.value{j}); +0297 if isKey(miriams,current) +0298 existing=miriams(current); +0299 else +0300 existing=[]; +0301 end +0302 miriams(current)=[existing;i]; +0303 end +0304 end +0305 end +0306 +0307 %Get all keys +0308 allMiriams=keys(miriams); 0309 -0310 %Print output -0311 EM='The following MIRIAM strings are associated to more than one unique metabolite name:'; -0312 dispEM(EM,false,allMiriams(hasMultiple),trimWarnings); -0313 end -0314 -0315 %Check if there are metabolites with different names but the same InChI -0316 %codes -0317 if isfield(model,'inchis') -0318 inchis=containers.Map(); -0319 for i=1:numel(model.mets) -0320 if ~isempty(model.inchis{i}) -0321 %Get existing metabolite indexes -0322 if isKey(inchis,model.inchis{i}) -0323 existing=inchis(model.inchis{i}); -0324 else -0325 existing=[]; -0326 end -0327 inchis(model.inchis{i})=[existing;i]; -0328 end -0329 end -0330 -0331 %Get all keys -0332 allInchis=keys(inchis); -0333 -0334 hasMultiple=false(numel(allInchis),1); -0335 for i=1:numel(allInchis) -0336 if numel(inchis(allInchis{i}))>1 -0337 %Check if they all have the same name -0338 if numel(unique(model.metNames(inchis(allInchis{i}))))>1 -0339 hasMultiple(i)=true; -0340 end -0341 end -0342 end -0343 -0344 %Print output -0345 EM='The following InChI strings are associated to more than one unique metabolite name:'; -0346 dispEM(EM,false,allInchis(hasMultiple),trimWarnings); -0347 end -0348 end -0349 -0350 function I=duplicates(strings) -0351 I=false(numel(strings),1); -0352 [J, K]=unique(strings); -0353 if numel(J)~=numel(strings) -0354 L=1:numel(strings); -0355 L(K)=[]; -0356 I(L)=true; -0357 end -0358 end +0310 hasMultiple=false(numel(allMiriams),1); +0311 for i=1:numel(allMiriams) +0312 if numel(miriams(allMiriams{i}))>1 +0313 %Check if they all have the same name +0314 if numel(unique(model.metNames(miriams(allMiriams{i}))))>1 +0315 if ~regexp(allMiriams{i},'^sbo\/SBO:') % SBO terms are expected to be multiple +0316 hasMultiple(i)=true; +0317 end +0318 end +0319 end +0320 end +0321 +0322 %Print output +0323 EM='The following MIRIAM strings are associated to more than one unique metabolite name:'; +0324 dispEM(EM,false,allMiriams(hasMultiple),trimWarnings); +0325 end +0326 +0327 %Check if there are metabolites with different names but the same InChI +0328 %codes +0329 if isfield(model,'inchis') +0330 inchis=containers.Map(); +0331 for i=1:numel(model.mets) +0332 if ~isempty(model.inchis{i}) +0333 %Get existing metabolite indexes +0334 if isKey(inchis,model.inchis{i}) +0335 existing=inchis(model.inchis{i}); +0336 else +0337 existing=[]; +0338 end +0339 inchis(model.inchis{i})=[existing;i]; +0340 end +0341 end +0342 +0343 %Get all keys +0344 allInchis=keys(inchis); +0345 +0346 hasMultiple=false(numel(allInchis),1); +0347 for i=1:numel(allInchis) +0348 if numel(inchis(allInchis{i}))>1 +0349 %Check if they all have the same name +0350 if numel(unique(model.metNames(inchis(allInchis{i}))))>1 +0351 hasMultiple(i)=true; +0352 end +0353 end +0354 end +0355 +0356 %Print output +0357 EM='The following InChI strings are associated to more than one unique metabolite name:'; +0358 dispEM(EM,false,allInchis(hasMultiple),trimWarnings); +0359 end +0360 end +0361 +0362 function I=duplicates(strings) +0363 I=false(numel(strings),1); +0364 [J, K]=unique(strings); +0365 if numel(J)~=numel(strings) +0366 L=1:numel(strings); +0367 L(K)=[]; +0368 I(L)=true; +0369 end +0370 end
Generated by m2html © 2005
\ No newline at end of file diff --git a/doc/core/compareModels.html b/doc/core/compareRxnsGenesMetsComps.html similarity index 95% rename from doc/core/compareModels.html rename to doc/core/compareRxnsGenesMetsComps.html index c7cebd24..5f8f0b07 100644 --- a/doc/core/compareModels.html +++ b/doc/core/compareRxnsGenesMetsComps.html @@ -2,9 +2,9 @@ "http://www.w3.org/TR/REC-html40/loose.dtd"> - Description of compareModels - - + Description of compareRxnsGenesMetsComps + + @@ -12,22 +12,22 @@ -
Home > core > compareModels.m
+
Home > core > compareRxnsGenesMetsComps.m
-

compareModels +

compareRxnsGenesMetsComps

PURPOSE ^

-
compareModels
+
compareRxnsGenesMetsComps

SYNOPSIS ^

-
function compStruct=compareModels(models,printResults)
+
function compStruct=compareRxnsGenesMetsComps(models,printResults)

DESCRIPTION ^

-
 compareModels
+
 compareRxnsGenesMetsComps
    Compares two or more models with respect to overlap in terms of genes,
    reactions, metabolites and compartments.
 
@@ -51,7 +51,7 @@ 
DESCRIPTION ^CROSS-REFERENCE INFORMATION ^

@@ -68,8 +68,8 @@ 
SUBFUNCTIONS ^function A=getElements(models,field)
  • function toCheck=getToCheck(models,field)
  • function I=checkField(A)
  • function printList(models,toCheck,nElements)
  • function nElements=checkStuff(A,toCheck)
    • 
 
 
    SOURCE CODE ^
    
-
    0001 function compStruct=compareModels(models,printResults)
-0002 % compareModels
+
    0001 function compStruct=compareRxnsGenesMetsComps(models,printResults)
+0002 % compareRxnsGenesMetsComps
 0003 %   Compares two or more models with respect to overlap in terms of genes,
 0004 %   reactions, metabolites and compartments.
 0005 %
@@ -93,7 +93,7 @@ 
    SOURCE CODE ^%           nElements   vector with the number of elements for each
 0024 %                       comparison
 0025 %
-0026 %   Usage: compStruct=compareModels(models,printResults)
+0026 %   Usage: compStruct=compareRxnsGenesMetsComps(models,printResults)
 0027 
 0028 if nargin<2
 0029     printResults=true;
diff --git a/doc/core/constructEquations.html b/doc/core/constructEquations.html
index 4d7d5ef5..eeb4da81 100644
--- a/doc/core/constructEquations.html
+++ b/doc/core/constructEquations.html
@@ -69,7 +69,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=buildEquation	buildEquation
  • getIndexes	getIndexes
  • sortModel	sortModel
    • 
 This function is called by:
 
+
  • addRxnsGenesMets	addRxnsGenesMets
  • compareRxnsGenesMetsComps	compareRxnsGenesMetsComps
  • followChanged	followChanged
  • followFluxes	followFluxes
  • printFluxes	printFluxes
  • printModelStats	printModelStats
    • 
 
 
 
diff --git a/doc/core/convertToIrrev.html b/doc/core/convertToIrrev.html
index 61376c46..dcb995f3 100644
--- a/doc/core/convertToIrrev.html
+++ b/doc/core/convertToIrrev.html
@@ -70,12 +70,12 @@ 
    SOURCE CODE ^%   Usage: irrevModel=convertToIrrev(model,rxns)
 0015 
 0016 if nargin<2
-0017     rxns=model.rxns;
-0018 end
-0019 
-0020 irrevModel=model;
+0017     I=true(numel(model.rxns),1);
+0018 else
+0019     I=getIndexes(model,rxns,'rxns',true);
+0020 end
 0021 
-0022 I=getIndexes(model,rxns,'rxns',true);
+0022 irrevModel=model;
 0023 
 0024 revIndexesBool=model.rev~=0 & I;
 0025 revIndexes=find(revIndexesBool);
diff --git a/doc/core/dispEM.html b/doc/core/dispEM.html
index 6d6c6fb1..1460b77c 100644
--- a/doc/core/dispEM.html
+++ b/doc/core/dispEM.html
@@ -49,7 +49,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • addGenesRaven	addGenesRaven
  • addMets	addMets
  • addRxns	addRxns
  • addRxnsGenesMets	addRxnsGenesMets
  • addTransport	addTransport
  • analyzeSampling	analyzeSampling
  • buildEquation	buildEquation
  • changeRxns	changeRxns
  • checkModelStruct	checkModelStruct
  • checkRxn	checkRxn
  • checkTasks	checkTasks
  • compareModels	compareModels
  • compareMultipleModels	compareMultipleModels
  • constructS	constructS
  • consumeSomething	consumeSomething
  • contractModel	contractModel
  • expandModel	expandModel
  • fillGaps	fillGaps
  • findGeneDeletions	findGeneDeletions
  • fitParameters	fitParameters
  • fitTasks	fitTasks
  • getElementalBalance	getElementalBalance
  • getEssentialRxns	getEssentialRxns
  • getExpressionStructure	getExpressionStructure
  • getFluxZ	getFluxZ
  • getMetsInComp	getMetsInComp
  • getMinNrFluxes	getMinNrFluxes
  • getModelFromHomology	getModelFromHomology
  • getRxnsInComp	getRxnsInComp
  • guessComposition	guessComposition
  • makeSomething	makeSomething
  • mapCompartments	mapCompartments
  • mergeCompartments	mergeCompartments
  • mergeModels	mergeModels
  • parseTaskList	parseTaskList
  • predictLocalization	predictLocalization
  • printFluxes	printFluxes
  • randomSampling	randomSampling
  • removeBadRxns	removeBadRxns
  • removeMets	removeMets
  • replaceMets	replaceMets
  • reporterMetabolites	reporterMetabolites
  • setParam	setParam
  • simplifyModel	simplifyModel
  • sortModel	sortModel
  • standardizeGrRules	standardizeGrRules
    • 
+
  • addGenesRaven	addGenesRaven
  • addMets	addMets
  • addRxns	addRxns
  • addRxnsGenesMets	addRxnsGenesMets
  • addTransport	addTransport
  • analyzeSampling	analyzeSampling
  • buildEquation	buildEquation
  • changeRxns	changeRxns
  • checkModelStruct	checkModelStruct
  • checkRxn	checkRxn
  • checkTasks	checkTasks
  • compareMultipleModels	compareMultipleModels
  • compareRxnsGenesMetsComps	compareRxnsGenesMetsComps
  • constructS	constructS
  • consumeSomething	consumeSomething
  • contractModel	contractModel
  • expandModel	expandModel
  • fillGaps	fillGaps
  • findGeneDeletions	findGeneDeletions
  • fitParameters	fitParameters
  • fitTasks	fitTasks
  • getElementalBalance	getElementalBalance
  • getEssentialRxns	getEssentialRxns
  • getExpressionStructure	getExpressionStructure
  • getFluxZ	getFluxZ
  • getMetsInComp	getMetsInComp
  • getMinNrFluxes	getMinNrFluxes
  • getModelFromHomology	getModelFromHomology
  • getRxnsInComp	getRxnsInComp
  • guessComposition	guessComposition
  • makeSomething	makeSomething
  • mapCompartments	mapCompartments
  • mergeCompartments	mergeCompartments
  • mergeModels	mergeModels
  • parseTaskList	parseTaskList
  • predictLocalization	predictLocalization
  • printFluxes	printFluxes
  • randomSampling	randomSampling
  • removeBadRxns	removeBadRxns
  • removeMets	removeMets
  • replaceMets	replaceMets
  • reporterMetabolites	reporterMetabolites
  • setParam	setParam
  • simplifyModel	simplifyModel
  • sortModel	sortModel
  • standardizeGrRules	standardizeGrRules
    • 
 
 
 
@@ -99,11 +99,13 @@ 
    SOURCE CODE ^end
 0043 end
 0044 if throwErrors==false
-0045     fprintf([errorText '\n']);
-0046 else
-0047     throw(MException('',errorText));
-0048 end
-0049 end
    
+0045     %Escape special characters, required for fprintf
+0046     errorText=regexprep(errorText,'(\\|\%|'')','\\$0');
+0047     fprintf([errorText '\n']);
+0048 else
+0049     throw(MException('',errorText));
+0050 end
+0051 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/core/index.html b/doc/core/index.html
index 49cc1fca..5da70d52 100644
--- a/doc/core/index.html
+++ b/doc/core/index.html
@@ -19,7 +19,7 @@ 
    Index for core
    
 
 
    Matlab files in this directory:
    
 
-
     FSEOFFSEOF: implements the algorithm of Flux Scanning based on Enforced Objective Flux. 
     addExchangeRxnsaddExchangeRxns 
     addGenesRavenaddGenesRaven 
     addMetsaddMets 
     addRxnsaddRxns 
     addRxnsGenesMetsaddRxnsGenesMets 
     addTransportaddTransport 
     analyzeSamplinganalyzeSampling 
     buildEquationbuildEquation 
     canConsumecanConsume 
     canProducecanProduce 
     changeGeneAssocchangeGeneAssoc 
     changeGrRuleschangeGrRules 
     changeRxnschangeRxns 
     checkModelStructcheckModelStruct 
     checkProductioncheckProduction 
     checkRxncheckRxn 
     checkTaskscheckTasks 
     compareModelscompareModels 
     compareMultipleModelscompareMultipleModels 
     constructEquationsconstructEquations 
     constructSconstructS 
     consumeSomethingconsumeSomething 
     contractModelcontractModel 
     convertToIrrevconvertToIrrev 
     copyToCompscopyToComps 
     deleteUnusedGenesdeleteUnusedGenes 
     dispEMdispEM 
     expandModelexpandModel 
     fillGapsfillGaps 
     findGeneDeletionsfindGeneDeletions 
     fitParametersfitParameters 
     fitTasksfitTasks 
     followChangedfollowChanged 
     followFluxesfollowFluxes 
     gapReportgapReport 
     generateNewIdsgenerateNewIds 
     getAllRxnsFromGenesgetAllRxnsFromGenes 
     getAllSubGraphsgetAllSubGraphs 
     getAllowedBoundsgetAllowedBounds 
     getElementalBalancegetElementalBalance 
     getEssentialRxnsgetEssentialRxns 
     getExchangeRxnsgetExchangeRxns 
     getExpressionStructuregetExpressionStructure 
     getFluxZgetFluxZ 
     getIndexesgetIndexes 
     getMetsInCompgetMetsInComp 
     getMinNrFluxesgetMinNrFluxes 
     getModelFromHomologygetModelFromHomology 
     getObjectiveStringgetObjectiveString 
     getRxnsInCompgetRxnsInComp 
     getTransportRxnsgetTransportRxns 
     guessCompositionguessComposition 
     haveFluxhaveFlux 
     makeSomethingmakeSomething 
     mapCompartmentsmapCompartments 
     mergeCompartmentsmergeCompartments 
     mergeModelsmergeModels 
     parseFormulasparseFormulas 
     parseRxnEquparseRxnEqu 
     parseTaskListparseTaskList 
     permuteModelpermuteModel 
     predictLocalizationpredictLocalization 
     printFluxesprintFluxes 
     printModelprintModel 
     printModelStatsprintModelStats 
     randomSamplingrandomSampling 
     removeBadRxnsremoveBadRxns 
     removeGenesremoveGenes 
     removeMetsremoveMets 
     removeReactionsremoveReactions 
     replaceMetsreplaceMets 
     reporterMetabolitesreporterMetabolites 
     setExchangeBoundssetExchangeBounds 
     setParamsetParam 
     simplifyModelsimplifyModel 
     sortModelsortModel 
     standardizeGrRulesstandardizeGrRules 
    
+ FSEOFFSEOF: implements the algorithm of Flux Scanning based on Enforced Objective Flux.  addExchangeRxnsaddExchangeRxns  addGenesRavenaddGenesRaven  addMetsaddMets  addRxnsaddRxns  addRxnsGenesMetsaddRxnsGenesMets  addTransportaddTransport  analyzeSamplinganalyzeSampling  buildEquationbuildEquation  canConsumecanConsume  canProducecanProduce  changeGeneAssocchangeGeneAssoc  changeGrRuleschangeGrRules  changeRxnschangeRxns  checkModelStructcheckModelStruct  checkProductioncheckProduction  checkRxncheckRxn  checkTaskscheckTasks  compareMultipleModelscompareMultipleModels  compareRxnsGenesMetsCompscompareRxnsGenesMetsComps  constructEquationsconstructEquations  constructSconstructS  consumeSomethingconsumeSomething  contractModelcontractModel  convertToIrrevconvertToIrrev  copyToCompscopyToComps  deleteUnusedGenesdeleteUnusedGenes  dispEMdispEM  expandModelexpandModel  fillGapsfillGaps  findGeneDeletionsfindGeneDeletions  fitParametersfitParameters  fitTasksfitTasks  followChangedfollowChanged  followFluxesfollowFluxes  gapReportgapReport  generateNewIdsgenerateNewIds  getAllRxnsFromGenesgetAllRxnsFromGenes  getAllSubGraphsgetAllSubGraphs  getAllowedBoundsgetAllowedBounds  getElementalBalancegetElementalBalance  getEssentialRxnsgetEssentialRxns  getExchangeRxnsgetExchangeRxns  getExpressionStructuregetExpressionStructure  getFluxZgetFluxZ  getIndexesgetIndexes  getMetsInCompgetMetsInComp  getMinNrFluxesgetMinNrFluxes  getModelFromHomologygetModelFromHomology  getObjectiveStringgetObjectiveString  getRxnsInCompgetRxnsInComp  getTransportRxnsgetTransportRxns  guessCompositionguessComposition  haveFluxhaveFlux  makeSomethingmakeSomething  mapCompartmentsmapCompartments  mergeCompartmentsmergeCompartments  mergeModelsmergeModels  parseFormulasparseFormulas  parseRxnEquparseRxnEqu  parseTaskListparseTaskList  permuteModelpermuteModel  predictLocalizationpredictLocalization  printFluxesprintFluxes  printModelprintModel  printModelStatsprintModelStats  randomSamplingrandomSampling  removeBadRxnsremoveBadRxns  removeGenesremoveGenes  removeMetsremoveMets  removeReactionsremoveReactions  replaceMetsreplaceMets  reporterMetabolitesreporterMetabolites  setExchangeBoundssetExchangeBounds  setParamsetParam  simplifyModelsimplifyModel  sortModelsortModel  standardizeGrRulesstandardizeGrRules 
 
 
 
diff --git a/doc/core/permuteModel.html b/doc/core/permuteModel.html
index e09feed4..32b608e1 100644
--- a/doc/core/permuteModel.html
+++ b/doc/core/permuteModel.html
@@ -30,12 +30,15 @@ 
    DESCRIPTION ^
     permuteModel
    Changes the order of the reactions or metabolites in a model
 
+   Input:
    model     a model structure
-   indexes   a vector with the same length as the number of reactions in the
-             model which gives the new order of reactions
-   type      'rxns' for reactions and 'mets' for metabolites
+   indexes   a vector with the same length as the number of items in the
+             model, which gives the new order of items
+   type      'rxns' for reactions, 'mets' for metabolites, 'genes' for
+             genes, 'comps' for compartments
 
-     newModel  an updated model structure
+     Output:
+   newModel  an updated model structure
 
      Usage: newModel=permuteModel(model, indexes, type)
    
 
@@ -56,114 +59,158 @@ 
    SOURCE CODE ^% permuteModel
 0003 %   Changes the order of the reactions or metabolites in a model
 0004 %
-0005 %   model     a model structure
-0006 %   indexes   a vector with the same length as the number of reactions in the
-0007 %             model which gives the new order of reactions
-0008 %   type      'rxns' for reactions and 'mets' for metabolites
-0009 %
-0010 %     newModel  an updated model structure
+0005 %   Input:
+0006 %   model     a model structure
+0007 %   indexes   a vector with the same length as the number of items in the
+0008 %             model, which gives the new order of items
+0009 %   type      'rxns' for reactions, 'mets' for metabolites, 'genes' for
+0010 %             genes, 'comps' for compartments
 0011 %
-0012 %     Usage: newModel=permuteModel(model, indexes, type)
-0013 
-0014 newModel=model;
-0015 indexes=indexes(:);
+0012 %     Output:
+0013 %   newModel  an updated model structure
+0014 %
+0015 %     Usage: newModel=permuteModel(model, indexes, type)
 0016 
-0017 if strcmp(type,'rxns')
-0018     if isfield(newModel,'rxns')
-0019         newModel.rxns=newModel.rxns(indexes);
-0020     end
-0021     if isfield(newModel,'lb')
-0022         newModel.lb=newModel.lb(indexes);
-0023     end
-0024     if isfield(newModel,'ub')
-0025         newModel.ub=newModel.ub(indexes);
-0026     end
-0027     if isfield(newModel,'rev')
-0028         newModel.rev=newModel.rev(indexes);
-0029     end
-0030     if isfield(newModel,'c')
-0031         newModel.c=newModel.c(indexes);
-0032     end
-0033     if isfield(newModel,'S')
-0034         newModel.S=newModel.S(:,indexes);
-0035     end
-0036     if isfield(newModel,'rxnNames')
-0037         newModel.rxnNames=newModel.rxnNames(indexes);
-0038     end
-0039     if isfield(newModel,'rxnGeneMat')
-0040         newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:);
-0041     end
-0042     if isfield(newModel,'grRules')
-0043         newModel.grRules=newModel.grRules(indexes);
-0044     end
-0045     if isfield(newModel,'subSystems')
-0046         newModel.subSystems=newModel.subSystems(indexes);
-0047     end
-0048     if isfield(newModel,'eccodes')
-0049         newModel.eccodes=newModel.eccodes(indexes);
-0050     end
-0051     if isfield(newModel,'equations')
-0052         newModel.equations=newModel.equations(indexes);
-0053     end
-0054     if isfield(newModel,'rxnMiriams')
-0055         newModel.rxnMiriams=newModel.rxnMiriams(indexes);
-0056     end
-0057     if isfield(newModel,'rxnComps')
-0058         newModel.rxnComps=newModel.rxnComps(indexes);
-0059     end
-0060     if isfield(newModel,'rxnFrom')
-0061         newModel.rxnFrom=newModel.rxnFrom(indexes);
-0062     end
-0063     if isfield(newModel,'rxnScores')
-0064         newModel.rxnScores=newModel.rxnScores(indexes);
-0065     end
-0066     if isfield(newModel,'rxnNotes')
-0067         newModel.rxnNotes=newModel.rxnNotes(indexes);
-0068     end
-0069     if isfield(newModel,'rxnReferences')
-0070         newModel.rxnReferences=newModel.rxnReferences(indexes);
-0071     end
-0072     if isfield(newModel,'rxnConfidenceScores')
-0073         newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes);
-0074     end
-0075 end
-0076 
-0077 if strcmp(type,'mets')
-0078     if isfield(newModel,'mets')
-0079         newModel.mets=newModel.mets(indexes);
-0080     end
-0081     if isfield(newModel,'metNames')
-0082         newModel.metNames=newModel.metNames(indexes);
-0083     end
-0084     if isfield(newModel,'b')
-0085         newModel.b=newModel.b(indexes,:);
-0086     end
-0087     if isfield(newModel,'metComps')
-0088         newModel.metComps=newModel.metComps(indexes);
-0089     end
-0090     if isfield(newModel,'S')
-0091         newModel.S=newModel.S(indexes,:);
-0092     end
-0093     if isfield(newModel,'unconstrained')
-0094         newModel.unconstrained=newModel.unconstrained(indexes);
-0095     end
-0096     if isfield(newModel,'metMiriams')
-0097         newModel.metMiriams=newModel.metMiriams(indexes,:);
-0098     end
-0099     if isfield(newModel,'inchis')
-0100         newModel.inchis=newModel.inchis(indexes);
-0101     end
-0102     if isfield(newModel,'metFormulas')
-0103         newModel.metFormulas=newModel.metFormulas(indexes);
-0104     end
-0105     if isfield(newModel,'metFrom')
-0106         newModel.metFrom=newModel.metFrom(indexes);
-0107     end
-0108     if isfield(newModel,'metCharges')
-0109         newModel.metCharges=newModel.metCharges(indexes);
-0110     end
-0111 end
-0112 end
    +0017 newModel=model; +0018 indexes=indexes(:); +0019 +0020 switch type +0021 case 'rxns' +0022 if isfield(newModel,'rxns') +0023 newModel.rxns=newModel.rxns(indexes); +0024 end +0025 if isfield(newModel,'lb') +0026 newModel.lb=newModel.lb(indexes); +0027 end +0028 if isfield(newModel,'ub') +0029 newModel.ub=newModel.ub(indexes); +0030 end +0031 if isfield(newModel,'rev') +0032 newModel.rev=newModel.rev(indexes); +0033 end +0034 if isfield(newModel,'c') +0035 newModel.c=newModel.c(indexes); +0036 end +0037 if isfield(newModel,'S') +0038 newModel.S=newModel.S(:,indexes); +0039 end +0040 if isfield(newModel,'rxnNames') +0041 newModel.rxnNames=newModel.rxnNames(indexes); +0042 end +0043 if isfield(newModel,'rxnGeneMat') +0044 newModel.rxnGeneMat=newModel.rxnGeneMat(indexes,:); +0045 end +0046 if isfield(newModel,'grRules') +0047 newModel.grRules=newModel.grRules(indexes); +0048 end +0049 if isfield(newModel,'subSystems') +0050 newModel.subSystems=newModel.subSystems(indexes); +0051 end +0052 if isfield(newModel,'eccodes') +0053 newModel.eccodes=newModel.eccodes(indexes); +0054 end +0055 if isfield(newModel,'equations') +0056 newModel.equations=newModel.equations(indexes); +0057 end +0058 if isfield(newModel,'rxnMiriams') +0059 newModel.rxnMiriams=newModel.rxnMiriams(indexes); +0060 end +0061 if isfield(newModel,'rxnComps') +0062 newModel.rxnComps=newModel.rxnComps(indexes); +0063 end +0064 if isfield(newModel,'rxnFrom') +0065 newModel.rxnFrom=newModel.rxnFrom(indexes); +0066 end +0067 if isfield(newModel,'rxnScores') +0068 newModel.rxnScores=newModel.rxnScores(indexes); +0069 end +0070 if isfield(newModel,'rxnNotes') +0071 newModel.rxnNotes=newModel.rxnNotes(indexes); +0072 end +0073 if isfield(newModel,'rxnReferences') +0074 newModel.rxnReferences=newModel.rxnReferences(indexes); +0075 end +0076 if isfield(newModel,'rxnConfidenceScores') +0077 newModel.rxnConfidenceScores=newModel.rxnConfidenceScores(indexes); +0078 end +0079 case 'mets' +0080 if isfield(newModel,'mets') +0081 newModel.mets=newModel.mets(indexes); +0082 end +0083 if isfield(newModel,'metNames') +0084 newModel.metNames=newModel.metNames(indexes); +0085 end +0086 if isfield(newModel,'b') +0087 newModel.b=newModel.b(indexes,:); +0088 end +0089 if isfield(newModel,'metComps') +0090 newModel.metComps=newModel.metComps(indexes); +0091 end +0092 if isfield(newModel,'S') +0093 newModel.S=newModel.S(indexes,:); +0094 end +0095 if isfield(newModel,'unconstrained') +0096 newModel.unconstrained=newModel.unconstrained(indexes); +0097 end +0098 if isfield(newModel,'metMiriams') +0099 newModel.metMiriams=newModel.metMiriams(indexes,:); +0100 end +0101 if isfield(newModel,'inchis') +0102 newModel.inchis=newModel.inchis(indexes); +0103 end +0104 if isfield(newModel,'metFormulas') +0105 newModel.metFormulas=newModel.metFormulas(indexes); +0106 end +0107 if isfield(newModel,'metFrom') +0108 newModel.metFrom=newModel.metFrom(indexes); +0109 end +0110 if isfield(newModel,'metCharges') +0111 newModel.metCharges=newModel.metCharges(indexes); +0112 end +0113 case 'genes' +0114 if isfield(newModel,'genes') +0115 newModel.genes=newModel.genes(indexes); +0116 end +0117 if isfield(newModel,'geneComps') +0118 newModel.geneComps=newModel.geneComps(indexes); +0119 end +0120 if isfield(newModel,'geneMiriams') +0121 newModel.geneMiriams=newModel.geneMiriams(indexes); +0122 end +0123 if isfield(newModel,'geneShortNames') +0124 newModel.geneShortNames=newModel.geneShortNames(indexes); +0125 end +0126 if isfield(newModel,'rxnGeneMat') +0127 newModel.rxnGeneMat=newModel.rxnGeneMat(:,indexes); +0128 end +0129 case 'comps' +0130 if isfield(newModel,'comps') +0131 newModel.comps=newModel.comps(indexes); +0132 end +0133 if isfield(newModel,'compNames') +0134 newModel.compNames=newModel.compNames(indexes); +0135 end +0136 if isfield(newModel,'compOutside') +0137 newModel.compOutside=newModel.compOutside(indexes); +0138 end +0139 if isfield(newModel,'compMiriams') +0140 newModel.compMiriams=newModel.compMiriams(indexes); +0141 end +0142 [~,J]=sort(indexes); % The *index* of compartment is used in next fields +0143 if isfield(newModel,'metComps') +0144 [toreplace, bywhat] = ismember(newModel.metComps,1:length(J)); +0145 newModel.metComps(toreplace) = J(bywhat(toreplace)); +0146 end +0147 if isfield(model,'rxnComps') +0148 [toreplace, bywhat] = ismember(model.rxnComps,1:length(J)); +0149 model.rxnComps(toreplace) = J(bywhat(toreplace)); +0150 end +0151 if isfield(model,'geneComps') +0152 [toreplace, bywhat] = ismember(model.geneComps,1:length(J)); +0153 model.geneComps(toreplace) = J(bywhat(toreplace)); +0154 end +0155 end +0156 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/external/getBlast.html b/doc/external/getBlast.html index 09ddcfcb..aecef88b 100644 --- a/doc/external/getBlast.html +++ b/doc/external/getBlast.html @@ -24,12 +24,12 @@

    PURPOSE ^getBlast

    SYNOPSIS ^

    -
    function blastStructure=getBlast(organismID,fastaFile,modelIDs,refFastaFiles)
    +
    function [blastStructure,blastReport]=getBlast(organismID,fastaFile,modelIDs,refFastaFiles,develMode,hideVerbose)

    DESCRIPTION ^

     getBlast
-   Performs a bidirectional BLASTP between the organism of interest and a
-   set of template organisms.
+   Performs a bidirectional BLAST between the organism of interest and a
+   set of template organisms
 
    Input:
    organismID      the id of the organism of interest. This should also
@@ -41,19 +41,27 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -68,144 +76,189 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^
    
-
    0001 function blastStructure=getBlast(organismID,fastaFile,modelIDs,refFastaFiles)
-0002 % getBlast
-0003 %   Performs a bidirectional BLASTP between the organism of interest and a
-0004 %   set of template organisms.
-0005 %
-0006 %   Input:
-0007 %   organismID      the id of the organism of interest. This should also
-0008 %                   match with the id supplied to getModelFromHomology
-0009 %   fastaFile       a FASTA file with the protein sequences for the
-0010 %                   organism of interest
-0011 %   modelIDs        a cell array of model ids. These must match the
-0012 %                   "model.id" fields in the "models" structure if the
-0013 %                   output is to be used with getModelFromHomology
-0014 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
-0015 %                   files
-0016 %
-0017 %   Output:
-0018 %   blastStructure  structure containing the bidirectional homology
-0019 %                   measurements which are used by getModelFromHomology
-0020 %
-0021 %   NOTE: This function calls BLASTP to perform a bidirectional homology
-0022 %   test between the organism of interest and a set of other organisms
-0023 %   using standard settings. The only filtering this functions does is the
-0024 %   removal of hits with E value higher than 10e-5. If you would like to
-0025 %   use other homology measurements, please see getBlastFromExcel.
-0026 %
-0027 %   Usage: blastStructure=getBlast(organismID,fastaFile,modelIDs,...
-0028 %           refFastaFiles)
-0029 
-0030 %Everything should be cell arrays
-0031 organismID=cellstr(organismID);
-0032 fastaFile=cellstr(fastaFile);
-0033 modelIDs=cellstr(modelIDs);
-0034 refFastaFiles=cellstr(refFastaFiles);
-0035 
-0036 blastStructure=[];
-0037 
-0038 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
-0039 %way to do this
-0040 [ST, I]=dbstack('-completenames');
-0041 ravenPath=fileparts(fileparts(ST(I).file));
-0042 
-0043 %Construct databases and output file
-0044 tmpDB=tempname;
-0045 outFile=tempname;
-0046 
-0047 %Check for existence of files. If no full path is specified for a file,
-0048 %assume that it is in the current folder
-0049 if isrow(refFastaFiles)
-0050     files=horzcat(fastaFile,refFastaFiles);
-0051 else
-0052     files=vertcat(fastaFile,refFastaFiles);
-0053 end
-0054 
-0055 files=checkFileExistence(files,true,false); %No whitespace allowed
-0056 fastaFile = files(1);
-0057 refFastaFiles = files(2:end);
-0058 
-0059 %Create a database for the new organism and blast each of the refFastaFiles
-0060 %against it
-0061 if isunix
-0062     if ismac
-0063         binEnd='.mac';
-0064     else
-0065         binEnd='';
-0066     end
-0067 elseif ispc
-0068     binEnd='';
-0069     setenv('BLASTDB_LMDB_MAP_SIZE','1000000');
-0070 else
-0071     dispEM('Unknown OS, exiting.')
-0072     return
-0073 end
-0074 
-0075 % Run BLAST multi-threaded to use all logical cores assigned to MATLAB.
-0076 cores = evalc('feature(''numcores'')');
-0077 cores = strsplit(cores, 'MATLAB was assigned: ');
-0078 cores = regexp(cores{2},'^\d*','match');
-0079 cores = cores{1};
+
    0001 function [blastStructure,blastReport]=getBlast(organismID,fastaFile,...
+0002     modelIDs,refFastaFiles,develMode,hideVerbose)
+0003 % getBlast
+0004 %   Performs a bidirectional BLAST between the organism of interest and a
+0005 %   set of template organisms
+0006 %
+0007 %   Input:
+0008 %   organismID      the id of the organism of interest. This should also
+0009 %                   match with the id supplied to getModelFromHomology
+0010 %   fastaFile       a FASTA file with the protein sequences for the
+0011 %                   organism of interest
+0012 %   modelIDs        a cell array of model ids. These must match the
+0013 %                   "model.id" fields in the "models" structure if the
+0014 %                   output is to be used with getModelFromHomology
+0015 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
+0016 %                   files
+0017 %   develMode       true if blastReport should be generated that is used
+0018 %                   in the unit testing function for BLAST+ (opt, default
+0019 %                   false)
+0020 %   hideVerbose     true if no status messages should be printed (opt,
+0021 %                   default false)
+0022 %
+0023 %   Output:
+0024 %   blastStructure  structure containing the bidirectional homology
+0025 %                   measurements that can be used by getModelFromHomology
+0026 %   blastReport     structure containing MD5 hashes for FASTA database
+0027 %                   files and non-parsed BLAST output data. Will be blank
+0028 %                   if develMode is false.
+0029 %
+0030 %   NOTE: This function calls BLAST+ to perform a bidirectional homology
+0031 %   test between the organism of interest and a set of other organisms
+0032 %   using standard settings. The only filtering this function does is the
+0033 %   removal of hits with an E-value higher than 10e-5. The other homology
+0034 %   measurements can be implemented using getBlastFromExcel.
+0035 %
+0036 %   Usage: [blastStructure,blastReport]=getBlast(organismID,fastaFile,...
+0037 %    modelIDs,refFastaFiles,develMode,hideVerbose)
+0038 
+0039 if nargin<5
+0040     develMode = false;
+0041 end
+0042 if nargin<6
+0043     hideVerbose = false;
+0044 end
+0045 
+0046 %Everything should be cell arrays
+0047 organismID=cellstr(organismID);
+0048 fastaFile=cellstr(fastaFile);
+0049 modelIDs=cellstr(modelIDs);
+0050 refFastaFiles=cellstr(refFastaFiles);
+0051 
+0052 %Create blank structures for results
+0053 blastStructure=[];
+0054 blastReport.dbHashes.phr={};
+0055 blastReport.dbHashes.pot={};
+0056 blastReport.dbHashes.psq={};
+0057 blastReport.dbHashes.pto={};
+0058 blastReport.blastTxtOutput={};
+0059 
+0060 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
+0061 %way to do this
+0062 [ST, I]=dbstack('-completenames');
+0063 ravenPath=fileparts(fileparts(ST(I).file));
+0064 
+0065 %Generate temporary names for BLAST databases and output files
+0066 tmpDB=tempname;
+0067 outFile=tempname;
+0068 
+0069 %Check for existence of files. If no full path is specified for a file,
+0070 %assume that it is in the current folder
+0071 if isrow(refFastaFiles)
+0072     files=horzcat(fastaFile,refFastaFiles);
+0073 else
+0074     files=vertcat(fastaFile,refFastaFiles);
+0075 end
+0076 
+0077 files=checkFileExistence(files,2); %Copy files to temp dir
+0078 fastaFile = files(1);
+0079 refFastaFiles = files(2:end);
 0080 
-0081 [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' fastaFile{1} '" -out "' tmpDB '" -dbtype prot']);
-0082 if status~=0
-0083     EM=['makeblastdb did not run successfully, error: ', num2str(status)];
-0084     dispEM(EM,true);
-0085 end
-0086 
-0087 for i=1:numel(refFastaFiles)
-0088     fprintf(['BLASTing "' modelIDs{i} '" against "' organismID{1} '"..\n']);
-0089     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' refFastaFiles{i} '" -out "' outFile '_' num2str(i) '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
-0090     if status~=0
-0091         EM=['blastp did not run successfully, error: ', num2str(status)];
-0092         dispEM(EM,true);
-0093     end
+0081 %Identify the operating system
+0082 if isunix
+0083     if ismac
+0084         binEnd='.mac';
+0085     else
+0086         binEnd='';
+0087     end
+0088 elseif ispc
+0089     binEnd='.exe';
+0090     setenv('BLASTDB_LMDB_MAP_SIZE','1000000');
+0091 else
+0092     dispEM('Unknown OS, exiting.')
+0093     return
 0094 end
-0095 delete([tmpDB '*']);
-0096 
-0097 %Then create a database for each of the reference organisms and blast the
-0098 %new organism against them
-0099 for i=1:numel(refFastaFiles)
-0100     fprintf(['BLASTing "' organismID{1} '" against "' modelIDs{i} '"..\n']);
-0101     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' refFastaFiles{i} '" -out "' tmpDB '" -dbtype prot']);
-0102     if status~=0
-0103         EM=['makeblastdb did not run successfully, error: ', num2str(status)];
-0104         dispEM(EM,true);
-0105     end
-0106     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' fastaFile{1} '" -out "' outFile '_r' num2str(i) '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
-0107     delete([tmpDB '*']);
-0108     if status~=0
-0109         EM=['blastp did not run successfully, error: ', num2str(status)];
-0110         dispEM(EM,true);
-0111     end
-0112 end
-0113 
-0114 %Done with the BLAST, do the parsing of the text files
-0115 for i=1:numel(refFastaFiles)*2
-0116     tempStruct=[];
-0117     if i<=numel(refFastaFiles)
-0118         tempStruct.fromId=modelIDs{i};
-0119         tempStruct.toId=organismID{1};
-0120         A=readtable([outFile '_' num2str(i)],'Delimiter',',','Format','%s%s%f%f%f%f%f');
-0121     else
-0122         tempStruct.fromId=organismID{1};
-0123         tempStruct.toId=modelIDs{i-numel(refFastaFiles)};
-0124         A=readtable([outFile '_r' num2str(i-numel(refFastaFiles))],'Delimiter',',','Format','%s%s%f%f%f%f%f');
-0125     end
-0126     tempStruct.fromGenes=A{:,1};
-0127     tempStruct.toGenes=A{:,2};
-0128     tempStruct.evalue=table2array(A(:,3));
-0129     tempStruct.identity=table2array(A(:,4));
-0130     tempStruct.aligLen=table2array(A(:,5));
-0131     tempStruct.bitscore=table2array(A(:,6));
-0132     tempStruct.ppos=table2array(A(:,7));
-0133     blastStructure=[blastStructure tempStruct];
-0134 end
-0135 
-0136 %Remove the old tempfiles
-0137 delete([outFile '*']);
-0138 end
    
+0095 
+0096 %Run BLAST multi-threaded to use all logical cores assigned to MATLAB
+0097 cores = evalc('feature(''numcores'')');
+0098 cores = strsplit(cores, 'MATLAB was assigned: ');
+0099 cores = regexp(cores{2},'^\d*','match');
+0100 cores = cores{1};
+0101 
+0102 %Create a database for the new organism and blast each of the refFastaFiles
+0103 %against it
+0104 [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in ' fastaFile{1} ' -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']);
+0105 if develMode
+0106     blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.phr'));
+0107     blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pot'));
+0108     blastReport.dbHashes.psq{numel(blastReport.dbHashes.psq)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.psq'));
+0109     blastReport.dbHashes.pto{numel(blastReport.dbHashes.pto)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pto'));
+0110 end
+0111 if status~=0
+0112     EM=['makeblastdb did not run successfully, error: ', num2str(status)];
+0113     dispEM(EM,true);
+0114 end
+0115 
+0116 for i=1:numel(refFastaFiles)
+0117     if ~hideVerbose
+0118         fprintf(['BLASTing "' modelIDs{i} '" against "' organismID{1} '"..\n']);
+0119     end
+0120     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query ' refFastaFiles{i} ' -out "' outFile '_' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
+0121     if develMode
+0122         blastReport.blastTxtOutput{numel(blastReport.blastTxtOutput)+1}=importdata([outFile '_' num2str(i)]);
+0123     end
+0124     if status~=0
+0125         EM=['blastp did not run successfully, error: ', num2str(status)];
+0126         dispEM(EM,true);
+0127     end
+0128 end
+0129 delete([tmpDB filesep 'tmpDB*']);
+0130 
+0131 %Then create a database for each of the reference organisms and blast the
+0132 %new organism against them
+0133 for i=1:numel(refFastaFiles)
+0134     if ~hideVerbose
+0135         fprintf(['BLASTing "' organismID{1} '" against "' modelIDs{i} '"..\n']);
+0136     end
+0137     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in ' refFastaFiles{i} ' -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']);
+0138     if status~=0
+0139         EM=['makeblastdb did not run successfully, error: ', num2str(status)];
+0140         dispEM(EM,true);
+0141     end
+0142     [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query ' fastaFile{1} ' -out "' outFile '_r' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
+0143     if develMode
+0144         blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.phr'));
+0145         blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pot'));
+0146         blastReport.dbHashes.psq{numel(blastReport.dbHashes.psq)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.psq'));
+0147         blastReport.dbHashes.pto{numel(blastReport.dbHashes.pto)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pto'));
+0148         blastReport.blastTxtOutput{numel(blastReport.blastTxtOutput)+1}=importdata([outFile '_r' num2str(i)]);
+0149     end    
+0150     if status~=0
+0151         EM=['blastp did not run successfully, error: ', num2str(status)];
+0152         dispEM(EM,true);
+0153     end
+0154     delete([tmpDB filesep 'tmpDB*']);
+0155 end
+0156 
+0157 %Done with the BLAST, do the parsing of the text files
+0158 for i=1:numel(refFastaFiles)*2
+0159     tempStruct=[];
+0160     if i<=numel(refFastaFiles)
+0161         tempStruct.fromId=modelIDs{i};
+0162         tempStruct.toId=organismID{1};
+0163         A=readtable([outFile '_' num2str(i)],'Delimiter',',','Format','%s%s%f%f%f%f%f');
+0164     else
+0165         tempStruct.fromId=organismID{1};
+0166         tempStruct.toId=modelIDs{i-numel(refFastaFiles)};
+0167         A=readtable([outFile '_r' num2str(i-numel(refFastaFiles))],'Delimiter',',','Format','%s%s%f%f%f%f%f');
+0168     end
+0169     tempStruct.fromGenes=A{:,1};
+0170     tempStruct.toGenes=A{:,2};
+0171     tempStruct.evalue=table2array(A(:,3));
+0172     tempStruct.identity=table2array(A(:,4));
+0173     tempStruct.aligLen=table2array(A(:,5));
+0174     tempStruct.bitscore=table2array(A(:,6));
+0175     tempStruct.ppos=table2array(A(:,7));
+0176     blastStructure=[blastStructure tempStruct];
+0177 end
+0178 
+0179 %Remove the old tempfiles
+0180 delete([outFile '*']);
+0181 %Remove the temp fasta files
+0182 delete(files{:})
+0183 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/external/getDiamond.html b/doc/external/getDiamond.html
index eda2386c..3fff175b 100644
--- a/doc/external/getDiamond.html
+++ b/doc/external/getDiamond.html
@@ -24,12 +24,12 @@ 
    PURPOSE ^getDiamond

    SYNOPSIS ^

    -
    function blastStructure=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles)
    +
    function [blastStructure,diamondReport]=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles,develMode,hideVerbose)

    DESCRIPTION ^

     getDiamond
-   Uses DIAMOND to performs a bidirectional BLASTP between the organism
-   of interest and a set of template organisms.
+   Uses DIAMOND to perform a bidirectional BLAST between the organism
+   of interest and a set of template organisms
 
    Input:
    organismID      the id of the organism of interest. This should also
@@ -41,20 +41,28 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -69,145 +77,180 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^
    
-
    0001 function blastStructure=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles)
-0002 % getDiamond
-0003 %   Uses DIAMOND to performs a bidirectional BLASTP between the organism
-0004 %   of interest and a set of template organisms.
-0005 %
-0006 %   Input:
-0007 %   organismID      the id of the organism of interest. This should also
-0008 %                   match with the id supplied to getModelFromHomology
-0009 %   fastaFile       a FASTA file with the protein sequences for the
-0010 %                   organism of interest
-0011 %   modelIDs        a cell array of model ids. These must match the
-0012 %                   "model.id" fields in the "models" structure if the
-0013 %                   output is to be used with getModelFromHomology
-0014 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
-0015 %                   files
-0016 %
-0017 %   Output:
-0018 %   blastStructure  structure containing the bidirectional homology
-0019 %                   measurements which are used by getModelFromHomology
-0020 %
-0021 %   NOTE: This function calls DIAMOND to perform a bidirectional homology
-0022 %   test between the organism of interest and a set of other organisms
-0023 %   using the '--more-sensitive' setting from DIAMOND. For the most
-0024 %   sensitive results, the use of getBlast() is adviced, however,
-0025 %   getDiamond() is a fast alternative (>15x faster). The blastStructure
-0026 %   generated is in the same format as those obtained from getBlast().
-0027 %
-0028 %   Usage: blastStructure=getDiamond(organismID,fastaFile,modelIDs,...
-0029 %           refFastaFiles)
-0030 
-0031 %Everything should be cell arrays
-0032 organismID=cellstr(organismID);
-0033 fastaFile=cellstr(fastaFile);
-0034 modelIDs=cellstr(modelIDs);
-0035 refFastaFiles=cellstr(refFastaFiles);
-0036 
-0037 blastStructure=[];
-0038 
-0039 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
-0040 %way to do this
-0041 [ST, I]=dbstack('-completenames');
-0042 ravenPath=fileparts(fileparts(ST(I).file));
-0043 
-0044 %Construct databases and output file
-0045 tmpDB=tempname;
-0046 outFile=tempname;
-0047 
-0048 %Check for existence of files. If no full path is specified for a file,
-0049 %assume that it is in the current folder
-0050 if isrow(refFastaFiles)
-0051     files=horzcat(fastaFile,refFastaFiles);
-0052 else
-0053     files=vertcat(fastaFile,refFastaFiles);
-0054 end
-0055 
-0056 files=checkFileExistence(files,true,false); %No whitespace allowed
-0057 fastaFile = files(1);
-0058 refFastaFiles = files(2:end);
-0059 
-0060 %Create a database for the new organism and blast each of the refFastaFiles
-0061 %against it
+
    0001 function [blastStructure,diamondReport]=getDiamond(organismID,fastaFile,...
+0002     modelIDs,refFastaFiles,develMode,hideVerbose)
+0003 % getDiamond
+0004 %   Uses DIAMOND to perform a bidirectional BLAST between the organism
+0005 %   of interest and a set of template organisms
+0006 %
+0007 %   Input:
+0008 %   organismID      the id of the organism of interest. This should also
+0009 %                   match with the id supplied to getModelFromHomology
+0010 %   fastaFile       a FASTA file with the protein sequences for the
+0011 %                   organism of interest
+0012 %   modelIDs        a cell array of model ids. These must match the
+0013 %                   "model.id" fields in the "models" structure if the
+0014 %                   output is to be used with getModelFromHomology
+0015 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
+0016 %                   files
+0017 %   develMode       true if blastReport should be generated that is used
+0018 %                   in the unit testing function for DIAMOND (opt, default
+0019 %                   false)
+0020 %   hideVerbose     true if no status messages should be printed (opt,
+0021 %                   default false)
+0022 %
+0023 %   Output:
+0024 %   blastStructure  structure containing the bidirectional homology
+0025 %                   measurements which are used by getModelFromHomology
+0026 %   diamondReport   structure containing MD5 hashes for FASTA database
+0027 %                   files and non-parsed BLAST output data. Will be blank
+0028 %                   if develMode is false.
+0029 %
+0030 %   NOTE: This function calls DIAMOND to perform a bidirectional homology
+0031 %   search between the organism of interest and a set of other organisms
+0032 %   using the '--more-sensitive' setting from DIAMOND. For the most
+0033 %   sensitive results, the use of getBlast() is adviced, however,
+0034 %   getDiamond() is a fast alternative (>15x faster). The blastStructure
+0035 %   generated is in the same format as those obtained from getBlast().
+0036 %
+0037 %   Usage: [blastStructure,diamondReport]=getDiamond(organismID,fastaFile,...
+0038 %    modelIDs,refFastaFiles,develMode,hideVerbose)
+0039 
+0040 if nargin<5
+0041     develMode = false;
+0042 end
+0043 if nargin<6
+0044     hideVerbose = false;
+0045 end
+0046 
+0047 %Everything should be cell arrays
+0048 organismID=cellstr(organismID);
+0049 fastaFile=cellstr(fastaFile);
+0050 modelIDs=cellstr(modelIDs);
+0051 refFastaFiles=cellstr(refFastaFiles);
+0052 
+0053 %Create blank structures for results
+0054 blastStructure=[];
+0055 diamondReport.dbHashes={};
+0056 diamondReport.diamondTxtOutput={};
+0057 
+0058 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
+0059 %way to do this
+0060 [ST, I]=dbstack('-completenames');
+0061 ravenPath=fileparts(fileparts(ST(I).file));
 0062 
-0063 if isunix
-0064     if ismac
-0065         binEnd='.mac';
-0066     else
-0067         binEnd='';
-0068     end
-0069 elseif ispc
-0070     binEnd='';
+0063 %Generate temporary names for DIAMOND databases and output files
+0064 tmpDB=tempname;
+0065 outFile=tempname;
+0066 
+0067 %Check for existence of files. If no full path is specified for a file,
+0068 %assume that it is in the current folder
+0069 if isrow(refFastaFiles)
+0070     files=horzcat(fastaFile,refFastaFiles);
 0071 else
-0072     dispEM('Unknown OS, exiting.')
-0073     return
-0074 end
-0075 
-0076 % Run BLAST multi-threaded to use all logical cores assigned to MATLAB.
-0077 cores = evalc('feature(''numcores'')');
-0078 cores = strsplit(cores, 'MATLAB was assigned: ');
-0079 cores = regexp(cores{2},'^\d*','match');
-0080 cores = cores{1};
-0081 
-0082 [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' tmpDB '"']);
-0083 if status~=0
-0084     EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
-0085     dispEM(EM,true);
-0086 end
-0087 
-0088 for i=1:numel(refFastaFiles)
-0089     fprintf(['Running DIAMOND blastp with "' modelIDs{i} '" against "' organismID{1} '"..\n']);
-0090     [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
-0091     if status~=0
-0092         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
-0093         dispEM(EM,true);
-0094     end
-0095 end
-0096 delete([tmpDB '*']);
-0097 
-0098 %Then create a database for each of the reference organisms and blast the
-0099 %new organism against them
-0100 for i=1:numel(refFastaFiles)
-0101     fprintf(['Running DIAMOND blastp with "' organismID{1} '" against "' modelIDs{i} '"..\n']);
-0102     [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' tmpDB '"']);
-0103     if status~=0
-0104         EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
-0105         dispEM(EM,true);
-0106     end
-0107     [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]);
-0108     delete([tmpDB '*']);
-0109     if status~=0
-0110         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
-0111         dispEM(EM,true);
-0112     end
-0113 end
-0114 
-0115 %Done with the DIAMOND blastp, do the parsing of the text files
-0116 for i=1:numel(refFastaFiles)*2
-0117     tempStruct=[];
-0118     if i<=numel(refFastaFiles)
-0119         tempStruct.fromId=modelIDs{i};
-0120         tempStruct.toId=organismID{1};
-0121         A=readtable([outFile '_' num2str(i)],'Delimiter','\t','Format','%s%s%f%f%f%f%f');
-0122     else
-0123         tempStruct.fromId=organismID{1};
-0124         tempStruct.toId=modelIDs{i-numel(refFastaFiles)};
-0125         A=readtable([outFile '_r' num2str(i-numel(refFastaFiles))],'Delimiter','\t','Format','%s%s%f%f%f%f%f');
-0126     end
-0127     tempStruct.fromGenes=A{:,1};
-0128     tempStruct.toGenes=A{:,2};
-0129     tempStruct.evalue=table2array(A(:,3));
-0130     tempStruct.identity=table2array(A(:,4));
-0131     tempStruct.aligLen=table2array(A(:,5));
-0132     tempStruct.bitscore=table2array(A(:,6));
-0133     tempStruct.ppos=table2array(A(:,7));
-0134     blastStructure=[blastStructure tempStruct];
-0135 end
-0136 
-0137 %Remove the old tempfiles
-0138 delete([outFile '*']);
-0139 end
    
+0072     files=vertcat(fastaFile,refFastaFiles);
+0073 end
+0074 
+0075 files=checkFileExistence(files,2); %Copy files to temp dir
+0076 fastaFile = files(1);
+0077 refFastaFiles = files(2:end);
+0078 
+0079 %Identify the operating system
+0080 if isunix
+0081     if ismac
+0082         binEnd='.mac';
+0083     else
+0084         binEnd='';
+0085     end
+0086 elseif ispc
+0087     binEnd='.exe';
+0088 else
+0089     dispEM('Unknown OS, exiting.')
+0090     return
+0091 end
+0092 
+0093 %Run DIAMOND multi-threaded to use all logical cores assigned to MATLAB.
+0094 cores = evalc('feature(''numcores'')');
+0095 cores = strsplit(cores, 'MATLAB was assigned: ');
+0096 cores = regexp(cores{2},'^\d*','match');
+0097 cores = cores{1};
+0098 
+0099 %Create a database for the new organism and blast each of the refFastaFiles
+0100 %against it
+0101 [status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' fullfile(tmpDB) '"']);
+0102 if develMode
+0103     diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message,'[a-f0-9]{32}','match'));
+0104 end
+0105 if status~=0
+0106     EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
+0107     dispEM(EM,true);
+0108 end
+0109 
+0110 for i=1:numel(refFastaFiles)
+0111     if ~hideVerbose
+0112         fprintf(['Running DIAMOND blastp with "' modelIDs{i} '" against "' organismID{1} '"..\n']);
+0113     end
+0114     [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
+0115     if develMode
+0116         diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_' num2str(i)]);
+0117     end
+0118     if status~=0
+0119         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
+0120         dispEM(EM,true);
+0121     end
+0122 end
+0123 delete([tmpDB filesep 'tmpDB*']);
+0124 
+0125 %Then create a database for each of the reference organisms and blast the
+0126 %new organism against them
+0127 for i=1:numel(refFastaFiles)
+0128     if ~hideVerbose
+0129         fprintf(['Running DIAMOND blastp with "' organismID{1} '" against "' modelIDs{i} '"..\n']);
+0130     end
+0131     [status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' fullfile(tmpDB) '"']);
+0132     if status~=0
+0133         EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
+0134         dispEM(EM,true);
+0135     end
+0136     [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]);
+0137     if develMode
+0138         diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message,'[a-f0-9]{32}','match'));
+0139         diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_r' num2str(i)]);
+0140     end
+0141     if status~=0
+0142         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
+0143         dispEM(EM,true);
+0144     end
+0145     delete([tmpDB filesep 'tmpDB*']);
+0146 end
+0147 
+0148 %Done with the DIAMOND blastp, do the parsing of the text files
+0149 for i=1:numel(refFastaFiles)*2
+0150     tempStruct=[];
+0151     if i<=numel(refFastaFiles)
+0152         tempStruct.fromId=modelIDs{i};
+0153         tempStruct.toId=organismID{1};
+0154         A=readtable([outFile '_' num2str(i)],'Delimiter','\t','Format','%s%s%f%f%f%f%f');
+0155     else
+0156         tempStruct.fromId=organismID{1};
+0157         tempStruct.toId=modelIDs{i-numel(refFastaFiles)};
+0158         A=readtable([outFile '_r' num2str(i-numel(refFastaFiles))],'Delimiter','\t','Format','%s%s%f%f%f%f%f');
+0159     end
+0160     tempStruct.fromGenes=A{:,1};
+0161     tempStruct.toGenes=A{:,2};
+0162     tempStruct.evalue=table2array(A(:,3));
+0163     tempStruct.identity=table2array(A(:,4));
+0164     tempStruct.aligLen=table2array(A(:,5));
+0165     tempStruct.bitscore=table2array(A(:,6));
+0166     tempStruct.ppos=table2array(A(:,7));
+0167     blastStructure=[blastStructure tempStruct];
+0168 end
+0169 
+0170 %Remove the old tempfiles
+0171 delete([outFile '*']);
+0172 %Remove the temp fasta files
+0173 delete(files{:})
+0174 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/external/kegg/constructMultiFasta.html b/doc/external/kegg/constructMultiFasta.html
index 980bfae6..0c9e4435 100644
--- a/doc/external/kegg/constructMultiFasta.html
+++ b/doc/external/kegg/constructMultiFasta.html
@@ -49,7 +49,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • getKEGGModelForOrganism	getKEGGModelForOrganism
    • 
+
  • getKEGGModelForOrganism	getKEGGModelForOrganism
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -149,86 +149,82 @@ 
    SOURCE CODE ^end
 0091     end
 0092 end
-0093 fprintf('COMPLETE\n');
+0093 fprintf('COMPLETE\n');    
 0094 
-0095 fprintf('Generating the KEGG Orthology specific multi-FASTA files... ');
+0095 fprintf('Generating the KEGG Orthology specific multi-FASTA files...   0%% complete');
 0096 %Loop through the reactions and print the corresponding sequences
-0097 progressFlag=0;
-0098 for i=1:numel(model.rxns)
-0099 
-0100     %Do not overwrite existing files
-0101     if ~exist(fullfile(outputDir,[model.rxns{i} '.fa']), 'file')
-0102         
-0103         %Get the positions in elementPositions for the involved genes
-0104         genesUsed=model.rxnGeneMat(i,:);
-0105         
-0106         %Open a file for this reaction. This saves empty files for KOs
-0107         %without genes
-0108         rxnfid=fopen(fullfile(outputDir,[model.rxns{i} '.fa']),'w');
-0109         
-0110         if any(genesUsed)
-0111             positions=genePositions(genesUsed~=0);
-0112             
-0113             %It could be that some genes were not found. Delete those
-0114             %elements
-0115             positions(positions==0)=[];
-0116             
-0117             %Print each sequence
-0118             for j=1:numel(positions)
-0119                 fseek(fid,elementPositions(positions(j)),-1);
-0120                 %Should check that it ends with a gene!!!! Check for eof
-0121                 if positions(j)<numel(elementPositions)
-0122                     str=fread(fid,[1 double(elementPositions(positions(j)+1))-double(elementPositions(positions(j)))-1],'*char');
-0123                     
-0124                     %If the string does not end with a line feed character
-0125                     if str(end)~=10
-0126                         str=[str fread(fid,[1 double(elementPositions(positions(j)+2))-double(elementPositions(positions(j)+1))],'*char')];
-0127                         
-0128                         %This is if we still have not found a new gene.
-0129                         %Maximal unluck. This whole check should be done
-0130                         %when elementPositions are calculated!
-0131                         if str(end)~=10
-0132                             %Skip this gene
-0133                             continue;
-0134                         end
-0135                     end
-0136                 else
-0137                     str=fread(fid,[1 inf],'*char');
-0138                 end
-0139                 fwrite(rxnfid,['>' str]);
-0140             end
-0141         end
-0142         fclose(rxnfid);
-0143     end
-0144     %Print the progress: no need to update this for every
-0145     %iteration, just report once 25%, 50% and 75% are done
-0146     if progressFlag==0 && i>numel(model.rxns)*0.25
-0147         fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(outputDir,'*.fa')))/numel(model.rxns))*100);
-0148         progressFlag=progressFlag+1;
-0149     elseif (progressFlag==1 && i>=numel(model.rxns)*0.5) || (progressFlag==2 && i>=numel(model.rxns)*0.75)
-0150         fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(outputDir,'*.fa')))/numel(model.rxns))*100);
-0151         progressFlag=progressFlag+1;
-0152     end
-0153 end
-0154 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+0097 for i=1:numel(model.rxns)
+0098 
+0099     %Do not overwrite existing files
+0100     if ~exist(fullfile(outputDir,[model.rxns{i} '.fa']), 'file')
+0101         
+0102         %Get the positions in elementPositions for the involved genes
+0103         genesUsed=model.rxnGeneMat(i,:);
+0104         
+0105         %Open a file for this reaction. This saves empty files for KOs
+0106         %without genes
+0107         rxnfid=fopen(fullfile(outputDir,[model.rxns{i} '.fa']),'w');
+0108         
+0109         if any(genesUsed)
+0110             positions=genePositions(genesUsed~=0);
+0111             
+0112             %It could be that some genes were not found. Delete those
+0113             %elements
+0114             positions(positions==0)=[];
+0115             
+0116             %Print each sequence
+0117             for j=1:numel(positions)
+0118                 fseek(fid,elementPositions(positions(j)),-1);
+0119                 %Should check that it ends with a gene!!!! Check for eof
+0120                 if positions(j)<numel(elementPositions)
+0121                     str=fread(fid,[1 double(elementPositions(positions(j)+1))-double(elementPositions(positions(j)))-1],'*char');
+0122                     
+0123                     %If the string does not end with a line feed character
+0124                     if str(end)~=10
+0125                         str=[str fread(fid,[1 double(elementPositions(positions(j)+2))-double(elementPositions(positions(j)+1))],'*char')];
+0126                         
+0127                         %This is if we still have not found a new gene.
+0128                         %Maximal unluck. This whole check should be done
+0129                         %when elementPositions are calculated!
+0130                         if str(end)~=10
+0131                             %Skip this gene
+0132                             continue;
+0133                         end
+0134                     end
+0135                 else
+0136                     str=fread(fid,[1 inf],'*char');
+0137                 end
+0138                 fwrite(rxnfid,['>' str]);
+0139             end
+0140         end
+0141         fclose(rxnfid);
+0142     end
+0143     %Print the progress
+0144     if rem(i-1,50) == 0
+0145         progress=num2str(i/numel(model.rxns));
+0146         progress=pad(progress,3,'left');
+0147         fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
+0148     end
+0149 end
+0150 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+0151 
+0152 %Close the source file
+0153 fclose(fid);
+0154 end
 0155 
-0156 %Close the source file
-0157 fclose(fid);
-0158 end
-0159 
-0160 function files=listFiles(directory)
-0161 %Supporter function to list the files in a directory and return them as a
-0162 %cell array
-0163 temp=dir(directory);
-0164 files=cell(numel(temp),1);
-0165 for i=1:numel(temp)
-0166     files{i}=temp(i,1).name;
-0167 end
-0168 files=strrep(files,'.fa','');
-0169 files=strrep(files,'.hmm','');
-0170 files=strrep(files,'.out','');
-0171 files=strrep(files,'.faw','');
-0172 end
    +0156 function files=listFiles(directory) +0157 %Supporter function to list the files in a directory and return them as a +0158 %cell array +0159 temp=dir(directory); +0160 files=cell(numel(temp),1); +0161 for i=1:numel(temp) +0162 files{i}=temp(i,1).name; +0163 end +0164 files=strrep(files,'.fa',''); +0165 files=strrep(files,'.hmm',''); +0166 files=strrep(files,'.out',''); +0167 files=strrep(files,'.faw',''); +0168 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/external/kegg/getKEGGModelForOrganism.html b/doc/external/kegg/getKEGGModelForOrganism.html index db647501..f98436a4 100644 --- a/doc/external/kegg/getKEGGModelForOrganism.html +++ b/doc/external/kegg/getKEGGModelForOrganism.html @@ -24,7 +24,7 @@

    PURPOSE ^getKEGGModelForOrganism

    SYNOPSIS ^

    -
    function model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,nSequences,seqIdentity)
    +
    function model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,nSequences,seqIdentity,globalModel)

    DESCRIPTION ^

     getKEGGModelForOrganism
@@ -67,7 +67,7 @@ 
    DESCRIPTION ^DESCRIPTION ^DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • constructMultiFasta	constructMultiFasta
  • getModelFromKEGG	getModelFromKEGG
  • getPhylDist	getPhylDist
  • getWSLpath	getWSLpath
    • 
 This function is called by:
 
@@ -308,7 +292,7 @@ 
    SOURCE CODE ^
    0001 function model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,...
 0002     outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,...
 0003     keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,...
-0004     nSequences,seqIdentity)
+0004     nSequences,seqIdentity,globalModel)
 0005 % getKEGGModelForOrganism
 0006 %   Reconstructs a genome-scale metabolic model based on protein homology
 0007 %   to the orthologies in KEGG. If the target species is not available in
@@ -349,7 +333,7 @@ 
    SOURCE CODE ^%                       the HMMs were trained on pro- or eukaryotic
 0043 %                       sequences, using a sequence similarity threshold of
 0044 %                       XXX %, fitting the KEGG version YY. E.g.
-0045 %                       euk100_kegg82. (opt, see note about fastaFile. Note
+0045 %                       euk90_kegg100. (opt, see note about fastaFile. Note
 0046 %                       that in order to rebuild the KEGG model from a
 0047 %                       database dump, as opposed to using the version
 0048 %                       supplied with RAVEN, you would still need to supply
@@ -406,1031 +390,953 @@ 
    SOURCE CODE ^%                       running CD-HIT (opt, default inf)
 0100 %   seqIdentity         sequence identity threshold in CD-HIT, referred as
 0101 %                       "global sequence identity" in CD-HIT User's Guide.
-0102 %                       The only possible options are 1 (100 %), 0.9 (90 %)
-0103 %                       and 0.5 (50 %). If other values are provided,
-0104 %                       CD-HIT is skipped (opt, default -1, i.e. CD-HIT is
-0105 %                       skipped)
-0106 %
-0107 %   Output:
-0108 %   model               the reconstructed model
-0109 %
-0110 %   PLEASE READ THIS: The input to this function can be confusing, because
-0111 %   it is intended to be run in parallel on a cluster or in multiple
-0112 %   sessions. It therefore saves a lot of intermediate results to storage.
-0113 %   This also serves the purpose of not having to do redundant
-0114 %   calculations. This, however, comes with the disadvantage of somewhat
-0115 %   trickier handling. This is what this function does:
-0116 %
-0117 %   1a. Loads files from a local KEGG FTP dump and constructs a general
-0118 %       RAVEN model representing the metabolic network. The functions
-0119 %       getRxnsFromKEGG, getGenesFromKEGG, getMetsFromKEGG summarise the
-0120 %       data into 'keggRxns.mat', 'keggGenes.mat' and 'keggMets.mat' files,
-0121 %       which are later merged into 'keggModel.mat' by getModelFromKEGG
-0122 %       function. The function getPhylDist generates 'keggPhylDist.mat'
-0123 %       file. KEGG FTP access requires a <a href="matlab:
-0124 %       web('http://www.bioinformatics.jp/en/keggftp.html')">license</a>.
-0125 %   1b. Generates protein FASTA files from the KEGG FTP dump (see 1a). One
-0126 %       multi-FASTA file for each KO in KEGG is generated.
-0127 %
-0128 %   The Step 1 has to be re-done every time KEGG updates their database (or
-0129 %   rather when the updates are large enough to warrant re-running this
-0130 %   part). Many users would probably never use this feature.
-0131 %
-0132 %   2a. Filters KO-specific protein sets. This is done by using the
-0133 %       settings "maxPhylDist" and "nSequences" to control which sequences
-0134 %       should be used for constructing Hidden Markov models (HMMs), and
-0135 %       later for matching your sequences to.
-0136 %       The most common alternatives here would be to use sequences from
-0137 %       only eukaryotes, only prokaryotes or all sequences in KEGG. As
-0138 %       explained in the README.md file, various sets of pre-trained hidden
-0139 %       Markov models are available at <a href="matlab:
-0140 %       web('http://biomet-toolbox.chalmers.se/index.php?page=downtools-raven')">BioMet
-0141 %       Toolbox</a>. This is normally the most convenient way, but if you
-0142 %       would like to use, for example, only fungal sequences for training
-0143 %       the HMMs then you need to re-run this step.
-0144 %   2b. KO-specific protein FASTA files are re-organised into
-0145 %       non-redundant protein sets with CD-HIT. The user can only set
-0146 %       seqIdentity parameter, which corresponds to '-c' parameter in
-0147 %       CD-HIT, described as "sequence identity threshold". The following
-0148 %       non-default parameter settings are used depending on seqIdentity
-0149 %       value:
-0150 %       __________________________________________________________________
-0151 %       |                           |         seqIdentity value          |
-0152 %       |                           --------------------------------------
-0153 %       |                           |  1.0   |  0.9   |  0.5   |    x    |
-0154 %       | CD-HIT parameters         -------------------------------------|
-0155 %       -----------------------------------------------------------------|
-0156 %       | Input Dataset (-i)        | raw    | cdh100 | cdh90  | raw     |
-0157 %       | Output Dataset (-o)       | cdh100 | cdh90  | cdh50  | cdhOth  |
-0158 %       | Sequence identity (-c)    | 1.0    | 0.9    | 0.5    | x       |
-0159 %       | word_length (-n)          | 5      | 5      | 4      | 2-5*    |
-0160 %       | Max available memory (-M) |               2000                 |
-0161 %       ------------------------------------------------------------------
-0162 %       * - word length depends from sequence identity value (see CD-HIT
-0163 %       manual for more details)
-0164 %
-0165 %       The table reads as follows: if seqIdentity is equal to 1, then
-0166 %       "cdh100" set is produced from raw set of proteins. If seqIdentity
-0167 %       is equal to 0.9, then "cdh90" is produced from "cdh100" proteins
-0168 %       set. When seqIdentity is equal to 0.5, "cdh50" is obtained from
-0169 %       "cdh90" protein set. Finally, if other seqIdentity value is used,
-0170 %       it is obtained directly from the raw set of proteins.
-0171 %   2c. Does a multi sequence alignment for multi-FASTA files obtained in
-0172 %       Step 2b for future use. MAFFT software with automatic selection of
-0173 %       alignment algorithm is used in this step ('--auto').
-0174 %   2d. Trains hidden Markov models using HMMer for each of the aligned
-0175 %       KO-specific FASTA files obtained in Step 2c. This is performed with
-0176 %       'hmmbuild' using the default settings.
-0177 %
-0178 %   Step 2 may be reasonable to be re-done if the user wants to tweak the
-0179 %   settings in proteins filtering, clustering, multi sequence alignment or
-0180 %   HMMs training steps. However, it requires to have KO-specific protein
-0181 %   FASTA files obtained in Step 1a. As such files are not provided in
-0182 %   RAVEN and BioMet ToolBox, the user can only generate these files from
-0183 %   KEGG FTP dump files, so KEGG FTP license is needed.
-0184 %
-0185 %   3a. Queries the HMMs with sequences for the organism you are making a
-0186 %       model for. This step uses both the output from step 1a and from 2d.
-0187 %       This is done with 'hmmsearch' function under default settings. The
-0188 %       significance threshold value set in 'cutOff' parameter is used
-0189 %       later when parsing '*.out' files to filter out KO hits with higher
-0190 %       value than 'cutOff' value. The results with passable E values are
-0191 %       summarised into KO-gene occurence matrix with E values in
-0192 %       intersections as 'koGeneMat'. The parameters 'minScoreRatioG' and
-0193 %       'minScoreRatioKO' are then applied to 'prune' KO-gene associations
-0194 %       (see the function descriptions above for more details). The
-0195 %       intersection values for these 'prunable' associations are converted
-0196 %       to zeroes.
-0197 %   3b. Constructs a model based on the pre-processed KO-gene association
-0198 %       matrix (koGeneMat). As the full KEGG model already has reaction-KO
-0199 %       relationships, KOs are converted into the query genes. The final
-0200 %       draft model contains only these reactions, which are associated
-0201 %       with KOs from koGeneMat. The reactions without the genes may also
-0202 %       be included, if the user set keepSpontaneous as 'true'.
-0203 %
-0204 %   The Step 3 is specific to the organism for which the model is
-0205 %   reconstructed.
-0206 %
-0207 %   In principle the function looks at which output that is already available
-0208 %   and runs only the parts that are required for step 3. This means
-0209 %   that (see the definition of the parameters for details):
-0210 %   -1a is only performed if there are no KEGG model files in the
-0211 %   RAVEN\external\kegg directory
-0212 %   -1b is only performed if not all required HMMs OR aligned FASTA files
-0213 %   OR multi-FASTA files exist in the defined dataDir. This means that this
-0214 %   step is skipped if the HMMs are downloaded from BioMet Toolbox instead
-0215 %   (see above). If not all files exist it will try to find
-0216 %   the KEGG database files in dataDir.
-0217 %   -2a is only performed if not all required HMMs OR aligned FASTA files
-0218 %   files exist in the defined dataDir. This means that this step is skipped
-0219 %   if the HMMs are downloaded from BioMet Toolbox instead (see above).
-0220 %   -2b is only performed if not all required HMMs exist in the defined
-0221 %   dataDir. This means that this step is skipped if the FASTA files or
-0222 %   HMMs are downloaded from BioMet Toolbox instead (see above).
-0223 %   -3a is performed for the required HMMs for which no corresponding .out
-0224 %   file exists in outDir. This is just a way to enable the function to be
-0225 %   run in parallel or to resume if interrupted.
-0226 %   -3b is always performed.
-0227 %
-0228 %   These steps are specific to the organism for which you are
-0229 %   reconstructing the model.
-0230 %
-0231 %   Regarding the whole pipeline, the function checks the output that is
-0232 %   already available and runs only the parts that are required for step 3.
-0233 %   This means that (see the definition of the parameters for details):
-0234 %   -1a is only performed if there are no KEGG model files in the
-0235 %   RAVEN\external\kegg directory.
-0236 %   -1b is only performed if any of required KOs do not have HMMs, aligned
-0237 %   FASTA files, clustered FASTA files and raw FASTA files in the defined
-0238 %   dataDir. This means that this step is skipped if the HMMs are
-0239 %   downloaded from BioMet Toolbox instead (see above). If not all files
-0240 %   exist it will try to find the KEGG database files in dataDir.
-0241 %   -2ab are only performed if any of required KOs do not have HMMs,
-0242 %   aligned FASTA files and clustered FASTA files in the defined dataDir.
-0243 %   This means that this step is skipped if the HMMs are downloaded from
-0244 %   BioMet Toolbox instead (see above).
-0245 %   -2c is only performed if any of required KOs do not have HMMs and
-0246 %   aligned FASTA files in the defined dataDir. This means that this step
-0247 %   is skipped if the HMMs are downloaded from BioMet Toolbox instead (see
-0248 %   above).
-0249 %   -2d is only performed if any of required KOs do not have HMMs exist in
-0250 %   the defined dataDir. This means that this step is skipped if the FASTA
-0251 %   files or HMMs are downloaded from BioMet Toolbox instead (see above).
-0252 %   -3a is performed for the required HMMs for which no corresponding .out
-0253 %   file exists in outDir. This is just a way to enable the function to be
-0254 %   run in parallel or to resume if interrupted.
-0255 %   -3b is always performed.
-0256 %
-0257 %   NOTE: it is also possible to obtain draft model from KEGG without
-0258 %   providing protein FASTA file for the target organism. In such case the
-0259 %   organism three-four letter abbreviation set as 'organismID' must exist
-0260 %   in the local KEGG database. In such case, the program just fetches all
-0261 %   the reactions, which are associated with given 'organismID'.
-0262 %
-0263 %   Usage: model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,...
-0264 %    outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,...
-0265 %    keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,...
-0266 %    nSequences,seqIdentity)
-0267 
-0268 if nargin<2
-0269     fastaFile=[];
+0102 %                       If -1 is provided, CD-HIT is skipped (opt, default 0.9)
+0103 %   globalModel         structure containing both model and KOModel
+0104 %                       structures as generated by getModelFromKEGG. These
+0105 %                       will otherwise be loaded by via getModelFromKEGG.
+0106 %                       Providing globalKEGGmodel can speed up model
+0107 %                       generation if getKEGGModelForOrganism is run
+0108 %                       multiple times for different strains. Example:
+0109 %                       [globalModel.model,globalModel.KOModel] = getModelFromKEGG;
+0110 %                       (opt, default empty, global model is loaded by
+0111 %                       getModelFromKEGG)
+0112 %
+0113 %   Output:
+0114 %   model               the reconstructed model
+0115 %
+0116 %   PLEASE READ THIS: The input to this function can be confusing, because
+0117 %   it is intended to be run in parallel on a cluster or in multiple
+0118 %   sessions. It therefore saves a lot of intermediate results to storage.
+0119 %   This also serves the purpose of not having to do redundant
+0120 %   calculations. This, however, comes with the disadvantage of somewhat
+0121 %   trickier handling. This is what this function does:
+0122 %
+0123 %   1a. Loads files from a local KEGG FTP dump and constructs a general
+0124 %       RAVEN model representing the metabolic network. The functions
+0125 %       getRxnsFromKEGG, getGenesFromKEGG, getMetsFromKEGG summarise the
+0126 %       data into 'keggRxns.mat', 'keggGenes.mat' and 'keggMets.mat' files,
+0127 %       which are later merged into 'keggModel.mat' by getModelFromKEGG
+0128 %       function. The function getPhylDist generates 'keggPhylDist.mat'
+0129 %       file. KEGG FTP access requires a <a href="matlab:
+0130 %       web('http://www.bioinformatics.jp/en/keggftp.html')">license</a>.
+0131 %   1b. Generates protein FASTA files from the KEGG FTP dump (see 1a). One
+0132 %       multi-FASTA file for each KO in KEGG is generated.
+0133 %
+0134 %   The Step 1 has to be re-done every time KEGG updates their database (or
+0135 %   rather when the updates are large enough to warrant re-running this
+0136 %   part). Many users would probably never use this feature.
+0137 %
+0138 %   2a. Filters KO-specific protein sets. This is done by using the
+0139 %       settings "maxPhylDist" and "nSequences" to control which sequences
+0140 %       should be used for constructing Hidden Markov models (HMMs), and
+0141 %       later for matching your sequences to.
+0142 %       The most common alternatives here would be to use sequences from
+0143 %       only eukaryotes, only prokaryotes or all sequences in KEGG. As
+0144 %       explained in the README.md file, various sets of pre-trained hidden
+0145 %       Markov models are available at <a href="matlab:
+0146 %       web('http://biomet-toolbox.chalmers.se/index.php?page=downtools-raven')">BioMet
+0147 %       Toolbox</a>. This is normally the most convenient way, but if you
+0148 %       would like to use, for example, only fungal sequences for training
+0149 %       the HMMs then you need to re-run this step.
+0150 %   2b. KO-specific protein FASTA files are re-organised into
+0151 %       non-redundant protein sets with CD-HIT. The user can only set
+0152 %       seqIdentity parameter, which corresponds to '-c' parameter in
+0153 %       CD-HIT, described as "sequence identity threshold". CD-HIT suggsted
+0154 %       sequence identity specific word_length (-n) parameters are used.
+0155 %   2c. Does a multi sequence alignment for multi-FASTA files obtained in
+0156 %       Step 2b for future use. MAFFT software with automatic selection of
+0157 %       alignment algorithm is used in this step ('--auto').
+0158 %   2d. Trains hidden Markov models using HMMer for each of the aligned
+0159 %       KO-specific FASTA files obtained in Step 2c. This is performed with
+0160 %       'hmmbuild' using the default settings.
+0161 %
+0162 %   Step 2 may be reasonable to be re-done if the user wants to tweak the
+0163 %   settings in proteins filtering, clustering, multi sequence alignment or
+0164 %   HMMs training steps. However, it requires to have KO-specific protein
+0165 %   FASTA files obtained in Step 1a. As such files are not provided in
+0166 %   RAVEN and BioMet ToolBox, the user can only generate these files from
+0167 %   KEGG FTP dump files, so KEGG FTP license is needed.
+0168 %
+0169 %   3a. Queries the HMMs with sequences for the organism you are making a
+0170 %       model for. This step uses both the output from step 1a and from 2d.
+0171 %       This is done with 'hmmsearch' function under default settings. The
+0172 %       significance threshold value set in 'cutOff' parameter is used
+0173 %       later when parsing '*.out' files to filter out KO hits with higher
+0174 %       value than 'cutOff' value. The results with passable E values are
+0175 %       summarised into KO-gene occurence matrix with E values in
+0176 %       intersections as 'koGeneMat'. The parameters 'minScoreRatioG' and
+0177 %       'minScoreRatioKO' are then applied to 'prune' KO-gene associations
+0178 %       (see the function descriptions above for more details). The
+0179 %       intersection values for these 'prunable' associations are converted
+0180 %       to zeroes.
+0181 %   3b. Constructs a model based on the pre-processed KO-gene association
+0182 %       matrix (koGeneMat). As the full KEGG model already has reaction-KO
+0183 %       relationships, KOs are converted into the query genes. The final
+0184 %       draft model contains only these reactions, which are associated
+0185 %       with KOs from koGeneMat. The reactions without the genes may also
+0186 %       be included, if the user set keepSpontaneous as 'true'.
+0187 %
+0188 %   The Step 3 is specific to the organism for which the model is
+0189 %   reconstructed.
+0190 %
+0191 %   In principle the function looks at which output that is already available
+0192 %   and runs only the parts that are required for step 3. This means
+0193 %   that (see the definition of the parameters for details):
+0194 %   -1a is only performed if there are no KEGG model files in the
+0195 %   RAVEN\external\kegg directory
+0196 %   -1b is only performed if not all required HMMs OR aligned FASTA files
+0197 %   OR multi-FASTA files exist in the defined dataDir. This means that this
+0198 %   step is skipped if the HMMs are downloaded from BioMet Toolbox instead
+0199 %   (see above). If not all files exist it will try to find
+0200 %   the KEGG database files in dataDir.
+0201 %   -2a is only performed if not all required HMMs OR aligned FASTA files
+0202 %   files exist in the defined dataDir. This means that this step is skipped
+0203 %   if the HMMs are downloaded from BioMet Toolbox instead (see above).
+0204 %   -2b is only performed if not all required HMMs exist in the defined
+0205 %   dataDir. This means that this step is skipped if the FASTA files or
+0206 %   HMMs are downloaded from BioMet Toolbox instead (see above).
+0207 %   -3a is performed for the required HMMs for which no corresponding .out
+0208 %   file exists in outDir. This is just a way to enable the function to be
+0209 %   run in parallel or to resume if interrupted.
+0210 %   -3b is always performed.
+0211 %
+0212 %   These steps are specific to the organism for which you are
+0213 %   reconstructing the model.
+0214 %
+0215 %   Regarding the whole pipeline, the function checks the output that is
+0216 %   already available and runs only the parts that are required for step 3.
+0217 %   This means that (see the definition of the parameters for details):
+0218 %   -1a is only performed if there are no KEGG model files in the
+0219 %   RAVEN\external\kegg directory.
+0220 %   -1b is only performed if any of required KOs do not have HMMs, aligned
+0221 %   FASTA files, clustered FASTA files and raw FASTA files in the defined
+0222 %   dataDir. This means that this step is skipped if the HMMs are
+0223 %   downloaded from BioMet Toolbox instead (see above). If not all files
+0224 %   exist it will try to find the KEGG database files in dataDir.
+0225 %   -2ab are only performed if any of required KOs do not have HMMs,
+0226 %   aligned FASTA files and clustered FASTA files in the defined dataDir.
+0227 %   This means that this step is skipped if the HMMs are downloaded from
+0228 %   BioMet Toolbox instead (see above).
+0229 %   -2c is only performed if any of required KOs do not have HMMs and
+0230 %   aligned FASTA files in the defined dataDir. This means that this step
+0231 %   is skipped if the HMMs are downloaded from BioMet Toolbox instead (see
+0232 %   above).
+0233 %   -2d is only performed if any of required KOs do not have HMMs exist in
+0234 %   the defined dataDir. This means that this step is skipped if the FASTA
+0235 %   files or HMMs are downloaded from BioMet Toolbox instead (see above).
+0236 %   -3a is performed for the required HMMs for which no corresponding .out
+0237 %   file exists in outDir. This is just a way to enable the function to be
+0238 %   run in parallel or to resume if interrupted.
+0239 %   -3b is always performed.
+0240 %
+0241 %   NOTE: it is also possible to obtain draft model from KEGG without
+0242 %   providing protein FASTA file for the target organism. In such case the
+0243 %   organism three-four letter abbreviation set as 'organismID' must exist
+0244 %   in the local KEGG database. In such case, the program just fetches all
+0245 %   the reactions, which are associated with given 'organismID'.
+0246 %
+0247 %   Usage: model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,...
+0248 %    outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,...
+0249 %    keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,...
+0250 %    nSequences,seqIdentity)
+0251 
+0252 if nargin<2
+0253     fastaFile=[];
+0254 end
+0255 if nargin<3
+0256     dataDir=[];
+0257 end
+0258 if nargin<4
+0259     outDir=[];
+0260 end
+0261 if isempty(outDir)
+0262     outDir=tempdir;
+0263     %Delete all *.out files if any exist
+0264     delete(fullfile(outDir,'*.out'));
+0265 elseif ~isstr(outDir)
+0266     error('outDir should be provided as string');
+0267 end
+0268 if nargin<5
+0269     keepSpontaneous=true;
 0270 end
-0271 if nargin<3
-0272     dataDir=[];
+0271 if nargin<6
+0272     keepUndefinedStoich=true;
 0273 end
-0274 if nargin<4
-0275     outDir=[];
+0274 if nargin<7
+0275     keepIncomplete=true;
 0276 end
-0277 if isempty(outDir)
-0278     outDir=tempdir;
-0279     %Delete all *.out files if any exist
-0280     delete(fullfile(outDir,'*.out'));
-0281 elseif ~isstr(outDir)
-0282     error('outDir should be provided as string');
-0283 end
-0284 if nargin<5
-0285     keepSpontaneous=true;
-0286 end
-0287 if nargin<6
-0288     keepUndefinedStoich=true;
-0289 end
-0290 if nargin<7
-0291     keepIncomplete=true;
+0277 if nargin<8
+0278     keepGeneral=false;
+0279 end
+0280 if nargin<9
+0281     cutOff=10^-50;
+0282 end
+0283 if nargin<10
+0284     minScoreRatioKO=0.3;
+0285 end
+0286 if nargin<11
+0287     minScoreRatioG=0.8;
+0288 end
+0289 if nargin<12
+0290     maxPhylDist=inf;
+0291     %Include all sequences for each reaction
 0292 end
-0293 if nargin<8
-0294     keepGeneral=false;
-0295 end
-0296 if nargin<9
-0297     cutOff=10^-50;
-0298 end
-0299 if nargin<10
-0300     minScoreRatioKO=0.3;
-0301 end
-0302 if nargin<11
-0303     minScoreRatioG=0.8;
-0304 end
-0305 if nargin<12
-0306     maxPhylDist=inf;
-0307     %Include all sequences for each reaction
-0308 end
-0309 if nargin<13
-0310     nSequences=inf;
-0311     %Include all sequences for each reaction
-0312 end
-0313 if nargin<14
-0314     seqIdentity=-1;
-0315     %CD-HIT is not used in the pipeline
-0316 end
-0317 
-0318 if isempty(fastaFile)
-0319     fprintf(['\n\n*** The model reconstruction from KEGG based on the annotation available for KEGG Species <strong>' organismID '</strong> ***\n\n']);
-0320 else
-0321     fprintf('\n\n*** The model reconstruction from KEGG based on the protein homology search against KEGG Orthology specific HMMs ***\n\n');
-0322     %Check if query fasta exists
-0323     fastaFile=checkFileExistence(fastaFile,true,false);
-0324 end
-0325 
-0326 %Run the external binaries multi-threaded to use all logical cores assigned
-0327 %to MATLAB
-0328 cores = evalc('feature(''numcores'')');
-0329 cores = strsplit(cores, 'MATLAB was assigned: ');
-0330 cores = regexp(cores{2},'^\d*','match');
-0331 cores = cores{1};
-0332 
-0333 %Get the directory for RAVEN Toolbox. This is to get the path to the third
-0334 %party software used
-0335 [ST, I]=dbstack('-completenames');
-0336 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
-0337 
-0338 %Checking if dataDir is consistent. It must point to pre-trained HMMs set,
-0339 %compatible with the the current RAVEN version. The user may have the
-0340 %required zip file already in working directory or have it extracted. If
-0341 %the zip file and directory is not here, it is downloaded from the cloud
-0342 if ~isempty(dataDir)
-0343     hmmOptions={'euk100_kegg94', ...
-0344         'euk90_kegg94', ...
-0345         'euk50_kegg94', ...
-0346         'prok100_kegg94', ...
-0347         'prok90_kegg94', ...
-0348         'prok50_kegg94'};
-0349     hmmLinks={'wbnghgtpgftb6pcw572bhkl9a8ekh32d', ...
-0350         '754bdz0965261fktzlwc77rcv7me87i6', ...
-0351         '5xwgv17cn099xn7bxo2dq5h1dsdxrhn7', ...
-0352         'azpn5lwrb4gind2mn5hnbmux0lao5vt5', ...
-0353         'j19ybilr7js34uisnss92gvq5g6lljkk', ...
-0354         'b5vn631jrwdzcj4uwmvbshe2ws3zoalm'};
-0355     if all(cellfun(@isempty,regexp(dataDir,strcat(hmmOptions,'$')))) %Check if dataDir ends with any of the hmmOptions
-0356         if ~exist(fullfile(dataDir,'keggdb','genes.pep'),'file') && ...
-0357                 ~exist(fullfile(dataDir,'fasta'),'dir') && ...
-0358                 ~exist(fullfile(dataDir,'aligned'),'dir') && ...
-0359                 ~exist(fullfile(dataDir,'hmms'),'dir')
-0360             EM='Pre-trained HMMs set is not recognised. It should match any of the following sets:';
-0361             disp(EM);
-0362             disp(hmmOptions);
-0363             error('Fatal error occured. See the details above');
-0364         end
-0365     else
-0366         if exist(dataDir,'dir') && exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
-0367             fprintf(['NOTE: Found <strong>' dataDir '</strong> directory with pre-trained HMMs, it will therefore be used during reconstruction\n']);
-0368         elseif ~exist(dataDir,'dir') && exist([dataDir,'.zip'],'file')
-0369             fprintf('Extracting the HMMs archive file... ');
-0370             unzip([dataDir,'.zip']);
-0371             fprintf('COMPLETE\n');
-0372         else
-0373             hmmIndex=regexp(dataDir,hmmOptions);
-0374             hmmIndex=~cellfun(@isempty,hmmIndex);
-0375             fprintf('Downloading the HMMs archive file... ');
-0376             try
-0377                 websave([dataDir,'.zip'],['https://chalmersuniversity.box.com/shared/static/',hmmLinks{hmmIndex},'.zip']);
-0378             catch ME
-0379                 if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
-0380                     error('Failed to download the HMMs archive file, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues')
-0381                 end
-0382             end
-0383             
-0384             fprintf('COMPLETE\n');
-0385             fprintf('Extracting the HMMs archive file... ');
-0386             unzip([dataDir,'.zip']);
-0387             fprintf('COMPLETE\n');
-0388         end
-0389         %Check if HMMs are extracted
-0390         if ~exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
-0391             EM=['The HMM files seem improperly extracted and not found in ',dataDir,'/hmms. Please remove ',dataDir,' folder and rerun getKEGGModelForOrganism'];
-0392             disp(EM);
-0393             error('Fatal error occured. See the details above');
-0394         end
-0395     end
-0396 end
-0397 
-0398 %Check if the fasta-file contains '/' or'\'. If not then it's probably just
-0399 %a file name. Expand to full path.
-0400 if any(fastaFile)
-0401     if ~any(strfind(fastaFile,'\')) && ~any(strfind(fastaFile,'/'))
-0402         fastaFile=which(fastaFile);
-0403     end
-0404     %Create the required sub-folders in dataDir if they dont exist
-0405     if ~exist(fullfile(dataDir,'keggdb'),'dir')
-0406         mkdir(dataDir,'keggdb');
-0407     end
-0408     if ~exist(fullfile(dataDir,'fasta'),'dir')
-0409         mkdir(dataDir,'fasta');
-0410     end
-0411     if ~exist(fullfile(dataDir,'aligned'),'dir')
-0412         mkdir(dataDir,'aligned');
-0413     end
-0414     if ~exist(fullfile(dataDir,'hmms'),'dir')
-0415         mkdir(dataDir,'hmms');
+0293 if nargin<13
+0294     nSequences=inf;
+0295     %Include all sequences for each reaction
+0296 end
+0297 if nargin<14
+0298     seqIdentity=0.9;
+0299 end
+0300 
+0301 if isempty(fastaFile)
+0302     fprintf(['\n\n*** The model reconstruction from KEGG based on the annotation available for KEGG Species <strong>' organismID '</strong> ***\n\n']);
+0303 else
+0304     fprintf('\n\n*** The model reconstruction from KEGG based on the protein homology search against KEGG Orthology specific HMMs ***\n\n');
+0305     %Check if query fasta exists
+0306     fastaFile=checkFileExistence(fastaFile,2); %Copy file to temp dir
+0307 end
+0308 
+0309 %Run the external binaries multi-threaded to use all logical cores assigned
+0310 %to MATLAB
+0311 cores = evalc('feature(''numcores'')');
+0312 cores = strsplit(cores, 'MATLAB was assigned: ');
+0313 cores = regexp(cores{2},'^\d*','match');
+0314 cores = cores{1};
+0315 
+0316 %Get the directory for RAVEN Toolbox. This is to get the path to the third
+0317 %party software used
+0318 [ST, I]=dbstack('-completenames');
+0319 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0320 
+0321 %Checking if dataDir is consistent. It must point to pre-trained HMMs set,
+0322 %compatible with the the current RAVEN version. The user may have the
+0323 %required zip file already in working directory or have it extracted. If
+0324 %the zip file and directory is not here, it is downloaded from the cloud
+0325 if ~isempty(dataDir)
+0326     hmmOptions={'euk90_kegg100','prok90_kegg100'};
+0327     if ~endsWith(dataDir,hmmOptions) %Check if dataDir ends with any of the hmmOptions.
+0328                                      %If not, then check whether the required folders exist anyway.
+0329         if ~exist(fullfile(dataDir,'keggdb','genes.pep'),'file') && ...
+0330                 ~exist(fullfile(dataDir,'fasta'),'dir') && ...
+0331                 ~exist(fullfile(dataDir,'aligned'),'dir') && ...
+0332                 ~exist(fullfile(dataDir,'hmms'),'dir')
+0333             error(['Pre-trained HMMs set is not recognised. If you want download RAVEN provided sets, it should match any of the following: ' strjoin(hmmOptions,' or ')])
+0334         end
+0335     else
+0336         if exist(dataDir,'dir') && exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
+0337             fprintf(['NOTE: Found <strong>' dataDir '</strong> directory with pre-trained HMMs, it will therefore be used during reconstruction\n']);
+0338         elseif ~exist(dataDir,'dir') && exist([dataDir,'.zip'],'file')
+0339             fprintf('Extracting the HMMs archive file... ');
+0340             unzip([dataDir,'.zip']);
+0341             fprintf('COMPLETE\n');
+0342         else
+0343             hmmIndex=strcmp(dataDir,hmmOptions);
+0344             if ~any(hmmIndex)
+0345                 error(['Pre-trained HMMs are only provided with proteins clustered at 90% sequence identity (i.e. prok90_kegg100 and euk90_kegg100). ' ...
+0346                     'Use either of these datasets, or otherwise download the relevant sequence data from KEGG to train HMMs with your desired sequence identity'])
+0347             else
+0348                 fprintf('Downloading the HMMs archive file... ');
+0349                 try
+0350                     websave([dataDir,'.zip'],['https://github.com/SysBioChalmers/RAVEN/releases/download/v2.6.0/',hmmOptions{hmmIndex},'.zip']);
+0351                 catch ME
+0352                     if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
+0353                         error('Failed to download the HMMs archive file, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues')
+0354                     end
+0355                 end
+0356             end
+0357             
+0358             fprintf('COMPLETE\n');
+0359             fprintf('Extracting the HMMs archive file... ');
+0360             unzip([dataDir,'.zip']);
+0361             fprintf('COMPLETE\n');
+0362         end
+0363         %Check if HMMs are extracted
+0364         if ~exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
+0365             error(['The HMM files seem improperly extracted and not found in ',dataDir,'/hmms. Please remove ',dataDir,' folder and rerun getKEGGModelForOrganism']);
+0366         end
+0367     end
+0368 end
+0369 
+0370 %Check if the fasta-file contains '/' or'\'. If not then it's probably just
+0371 %a file name. Expand to full path.
+0372 if any(fastaFile)
+0373     if ~any(strfind(fastaFile,'\')) && ~any(strfind(fastaFile,'/'))
+0374         fastaFile=which(fastaFile);
+0375     end
+0376     %Create the required sub-folders in dataDir if they dont exist
+0377     if ~exist(fullfile(dataDir,'keggdb'),'dir')
+0378         mkdir(dataDir,'keggdb');
+0379     end
+0380     if ~exist(fullfile(dataDir,'fasta'),'dir')
+0381         mkdir(dataDir,'fasta');
+0382     end
+0383     if ~exist(fullfile(dataDir,'aligned'),'dir')
+0384         mkdir(dataDir,'aligned');
+0385     end
+0386     if ~exist(fullfile(dataDir,'hmms'),'dir')
+0387         mkdir(dataDir,'hmms');
+0388     end
+0389     if ~exist(outDir,'dir')
+0390         mkdir(outDir);
+0391     end
+0392 end
+0393 
+0394 %First generate the full global KEGG model. Can be provided as input.
+0395 %Otherwise, getModelFromKEGG is run. The dataDir must not be supplied as
+0396 %there is also an internal RAVEN version available
+0397 if nargin==15
+0398     model=globalModel.model;
+0399     KOModel=globalModel.KOModel;
+0400 elseif any(dataDir)
+0401     [model, KOModel]=getModelFromKEGG(fullfile(dataDir,'keggdb'),keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
+0402 else
+0403     [model, KOModel]=getModelFromKEGG([],keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
+0404 end
+0405 model.id=organismID;
+0406 model.c=zeros(numel(model.rxns),1);
+0407 
+0408 %If no FASTA file is supplied, then just remove all genes which are not for
+0409 %the given organism ID
+0410 if isempty(fastaFile)
+0411     %Check if organismID can be found in KEGG species list or is
+0412     %set to "eukaryotes" or "prokaryotes"
+0413     phylDistsFull=getPhylDist(fullfile(dataDir,'keggdb'),true);
+0414     if ~ismember(organismID,[phylDistsFull.ids 'eukaryotes' 'prokaryotes'])
+0415         error('Provided organismID is incorrect. Only species abbreviations from KEGG Species List or "eukaryotes"/"prokaryotes" are allowed.');
 0416     end
-0417     if ~exist(outDir,'dir')
-0418         mkdir(outDir);
-0419     end
-0420 end
-0421 
-0422 %First generate the full KEGG model. The dataDir must not be supplied as
-0423 %there is also an internal RAVEN version available
-0424 if any(dataDir)
-0425     [model, KOModel]=getModelFromKEGG(fullfile(dataDir,'keggdb'),keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
-0426 else
-0427     [model, KOModel]=getModelFromKEGG([],keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
-0428 end
-0429 model.id=organismID;
-0430 model.c=zeros(numel(model.rxns),1);
-0431 
-0432 %If no FASTA file is supplied, then just remove all genes which are not for
-0433 %the given organism ID
-0434 if isempty(fastaFile)
-0435     fprintf(['Pruning the model from <strong>non-' organismID '</strong> genes... ']);
-0436     if ismember(organismID,{'eukaryotes','prokaryotes'})
-0437         phylDists=getPhylDist(fullfile(dataDir,'keggdb'),maxPhylDist==-1);
-0438         if strcmp(organismID,'eukaryotes')
-0439             proxyid='hsa';
-0440             %Use H. sapiens here
-0441         else
-0442             proxyid='eco';
-0443             %Use E. coli here
-0444         end
-0445         [~, phylDistId]=ismember(proxyid,phylDists.ids);
-0446         idsToKeep=phylDists.ids(~isinf(phylDists.distMat(phylDistId,:)));
-0447         taxIDs=cellfun(@(x) x{1},cellfun(@(x) strsplit(x,':'),model.genes,'UniformOutput',false),'UniformOutput',false);
-0448         I=ismember(upper(taxIDs),upper(idsToKeep));
-0449     else
-0450         %KEGG organism IDs may have three or four letters
-0451         organismID=strcat(organismID,':');
-0452         %Add colon for accurate matching
-0453         if length(organismID)==4
-0454             I=cellfun(@(x) strcmpi(x(1:4),organismID),model.genes);
-0455         elseif length(organismID)==5
-0456             I=cellfun(@(x) strcmpi(x(1:5),organismID),model.genes);
-0457         end
-0458     end
-0459     %Remove those genes
-0460     model.genes=model.genes(I);
-0461     model.rxnGeneMat=model.rxnGeneMat(:,I);
-0462     fprintf('COMPLETE\n');
-0463 end
-0464 
-0465 %First remove all reactions without genes
-0466 if keepSpontaneous==true
-0467     fprintf('Removing non-spontaneous reactions without GPR rules... ');
-0468     load(fullfile(ravenPath,'external','kegg','keggRxns.mat'),'isSpontaneous');
-0469     I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous);
-0470     spontRxnsWithGenes=model.rxns(any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous));
-0471 else
-0472     fprintf('Removing reactions without GPR rules... ');
-0473     I=~any(model.rxnGeneMat,2);
-0474 end
-0475 model=removeReactions(model,I,true);
-0476 fprintf('COMPLETE\n');
-0477 
-0478 %Clean gene names
-0479 fprintf('Fixing gene names in the model... ');
-0480 for i=1:numel(model.genes)
-0481     %First get rid of the prefix organism id
-0482     model.genes{i}=model.genes{i}(strfind(model.genes{i},':')+1:end);
-0483     %Find and remove the description in parentheses if any
-0484     s=strfind(model.genes{i},'(');
-0485     if any(s)
-0486         model.genes{i}=model.genes{i}(1:s-1);
-0487     end
-0488 end
-0489 fprintf('COMPLETE\n');
-0490 
-0491 %If no FASTA file is supplied, then we are done here
-0492 if isempty(fastaFile)
-0493     %Create grRules
-0494     fprintf('Constructing GPR associations and annotations for the model... ');
-0495     model.grRules=cell(numel(model.rxns),1);
-0496     model.grRules(:)={''};
-0497     %Add the gene associations as 'or'
-0498     for i=1:numel(model.rxns)
-0499         %Find the involved genes
-0500         I=find(model.rxnGeneMat(i,:));
-0501         if any(I)
-0502             model.grRules{i}=['(' model.genes{I(1)}];
-0503             for j=2:numel(I)
-0504                 model.grRules{i}=[model.grRules{i} ' or ' model.genes{I(j)}];
-0505             end
-0506             model.grRules{i}=[model.grRules{i} ')'];
-0507         end
-0508     end
-0509     %Fix grRules and reconstruct rxnGeneMat
-0510     [grRules,rxnGeneMat] = standardizeGrRules(model); %Give detailed output
-0511     model.grRules = grRules;
-0512     model.rxnGeneMat = rxnGeneMat;
-0513     %Add geneMiriams, assuming that it follows the syntax
-0514     %kegg.genes/organismID:geneName
-0515     model.geneMiriams='';
-0516     for i=1:numel(model.genes)
-0517         model.geneMiriams{i,1}.name{1,1}='kegg.genes';
-0518         model.geneMiriams{i,1}.value{1,1}=strcat(lower(organismID),model.genes{i,1});
-0519     end
-0520     %Add the description to the reactions
-0521     for i=1:numel(model.rxns)
-0522         if ~isempty(model.rxnNotes{i})
-0523             model.rxnNotes(i)=strcat('Included by getKEGGModelForOrganism (without HMMs).',model.rxnNotes(i));
-0524             model.rxnNotes(i)=strrep(model.rxnNotes(i),'.','. ');
-0525         else
-0526             model.rxnNotes(i)={'Included by getKEGGModelForOrganism (without HMMs)'};
-0527         end
-0528     end
-0529     fprintf('COMPLETE\n\n');
-0530     fprintf('*** Model reconstruction complete ***\n');
-0531     return;
-0532 end
+0417     
+0418     fprintf(['Pruning the model from <strong>non-' organismID '</strong> genes... ']);
+0419     if ismember(organismID,{'eukaryotes','prokaryotes'})
+0420         phylDists=getPhylDist(fullfile(dataDir,'keggdb'),maxPhylDist==-1);
+0421         if strcmp(organismID,'eukaryotes')
+0422             proxyid='hsa';
+0423             %Use H. sapiens here
+0424         else
+0425             proxyid='eco';
+0426             %Use E. coli here
+0427         end
+0428         [~, phylDistId]=ismember(proxyid,phylDists.ids);
+0429         idsToKeep=phylDists.ids(~isinf(phylDists.distMat(phylDistId,:)));
+0430         taxIDs=cellfun(@(x) x{1},cellfun(@(x) strsplit(x,':'),model.genes,'UniformOutput',false),'UniformOutput',false);
+0431         I=ismember(upper(taxIDs),upper(idsToKeep));
+0432     else
+0433         %KEGG organism IDs may have three or four letters
+0434         organismID=strcat(organismID,':');
+0435         %Add colon for accurate matching
+0436         if length(organismID)==4
+0437             I=cellfun(@(x) strcmpi(x(1:4),organismID),model.genes);
+0438         elseif length(organismID)==5
+0439             I=cellfun(@(x) strcmpi(x(1:5),organismID),model.genes);
+0440         end
+0441     end
+0442     %Remove those genes
+0443     model.genes=model.genes(I);
+0444     model.rxnGeneMat=model.rxnGeneMat(:,I);
+0445     fprintf('COMPLETE\n');
+0446 end
+0447 
+0448 %First remove all reactions without genes
+0449 if keepSpontaneous==true
+0450     fprintf('Removing non-spontaneous reactions without GPR rules... ');
+0451     load(fullfile(ravenPath,'external','kegg','keggRxns.mat'),'isSpontaneous');
+0452     I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous);
+0453     spontRxnsWithGenes=model.rxns(any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous));
+0454 else
+0455     fprintf('Removing reactions without GPR rules... ');
+0456     I=~any(model.rxnGeneMat,2);
+0457 end
+0458 model=removeReactions(model,I,true);
+0459 fprintf('COMPLETE\n');
+0460 
+0461 %Clean gene names
+0462 fprintf('Fixing gene names in the model... ');
+0463 %Get rid of the prefix organism id
+0464 model.genes=regexprep(model.genes,'^\w+?:','');
+0465 fprintf('COMPLETE\n');
+0466 
+0467 %If no FASTA file is supplied, then we are done here
+0468 if isempty(fastaFile)
+0469     %Create grRules
+0470     fprintf('Constructing GPR associations and annotations for the model... ');
+0471     model.grRules=cell(numel(model.rxns),1);
+0472     model.grRules(:)={''};
+0473     %Add the gene associations as 'or'
+0474     for i=1:numel(model.rxns)
+0475         %Find the involved genes
+0476         I=find(model.rxnGeneMat(i,:));
+0477         if any(I)
+0478             model.grRules{i}=['(' model.genes{I(1)}];
+0479             for j=2:numel(I)
+0480                 model.grRules{i}=[model.grRules{i} ' or ' model.genes{I(j)}];
+0481             end
+0482             model.grRules{i}=[model.grRules{i} ')'];
+0483         end
+0484     end
+0485     %Fix grRules and reconstruct rxnGeneMat
+0486     [grRules,rxnGeneMat] = standardizeGrRules(model); %Give detailed output
+0487     model.grRules = grRules;
+0488     model.rxnGeneMat = rxnGeneMat;
+0489     %Add geneMiriams, assuming that it follows the syntax
+0490     %kegg.genes/organismID:geneName
+0491     model.geneMiriams='';
+0492     for i=1:numel(model.genes)
+0493         model.geneMiriams{i,1}.name{1,1}='kegg.genes';
+0494         model.geneMiriams{i,1}.value{1,1}=strcat(lower(organismID),model.genes{i,1});
+0495     end
+0496     %Add the description to the reactions
+0497     for i=1:numel(model.rxns)
+0498         if ~isempty(model.rxnNotes{i})
+0499             model.rxnNotes(i)=strcat('Included by getKEGGModelForOrganism (without HMMs).',model.rxnNotes(i));
+0500             model.rxnNotes(i)=strrep(model.rxnNotes(i),'.','. ');
+0501         else
+0502             model.rxnNotes(i)={'Included by getKEGGModelForOrganism (without HMMs)'};
+0503         end
+0504     end
+0505     fprintf('COMPLETE\n\n');
+0506     fprintf('*** Model reconstruction complete ***\n');
+0507     return;
+0508 end
+0509 
+0510 %Create a phylogenetic distance structure
+0511 phylDistStruct=getPhylDist(fullfile(dataDir,'keggdb'),maxPhylDist==-1);
+0512 [~, phylDistId]=ismember(model.id,phylDistStruct.ids);
+0513 
+0514 %Calculate the real maximal distance now. An abitary large number of 1000
+0515 %is used for the "all in kingdom" or "all sequences" options. This is a bit
+0516 %inconvenient way to do it, but it is to make it fit with some older code
+0517 if isinf(maxPhylDist) || maxPhylDist==-1
+0518     maxPhylDist=1000;
+0519 end
+0520 
+0521 %Get the KO ids for which files have been generated. Maybe not the neatest
+0522 %way..
+0523 fastaFiles=listFiles(fullfile(dataDir,'fasta','*.fa'));
+0524 alignedFiles=listFiles(fullfile(dataDir,'aligned','*.fa'));
+0525 alignedWorking=listFiles(fullfile(dataDir,'aligned','*.faw'));
+0526 hmmFiles=listFiles(fullfile(dataDir,'hmms','*.hmm'));
+0527 outFiles=listFiles(fullfile(outDir,'*.out'));
+0528 
+0529 %Check if multi-FASTA files should be generated. This should only be
+0530 %performed if there are IDs in the KOModel structure that haven't been
+0531 %parsed yet
+0532 missingFASTA=setdiff(KOModel.rxns,[fastaFiles;alignedFiles;hmmFiles;outFiles]);
 0533 
-0534 %Create a phylogenetic distance structure
-0535 phylDistStruct=getPhylDist(fullfile(dataDir,'keggdb'),maxPhylDist==-1);
-0536 [~, phylDistId]=ismember(model.id,phylDistStruct.ids);
-0537 
-0538 %Calculate the real maximal distance now. An abitary large number of 1000
-0539 %is used for the "all in kingdom" or "all sequences" options. This is a bit
-0540 %inconvenient way to do it, but it is to make it fit with some older code
-0541 if isinf(maxPhylDist) || maxPhylDist==-1
-0542     maxPhylDist=1000;
-0543 end
-0544 
-0545 %Get the KO ids for which files have been generated. Maybe not the neatest
-0546 %way..
-0547 fastaFiles=listFiles(fullfile(dataDir,'fasta','*.fa'));
-0548 alignedFiles=listFiles(fullfile(dataDir,'aligned','*.fa'));
-0549 alignedWorking=listFiles(fullfile(dataDir,'aligned','*.faw'));
-0550 hmmFiles=listFiles(fullfile(dataDir,'hmms','*.hmm'));
-0551 outFiles=listFiles(fullfile(outDir,'*.out'));
-0552 
-0553 %Check if multi-FASTA files should be generated. This should only be
-0554 %performed if there are IDs in the KOModel structure that haven't been
-0555 %parsed yet
-0556 missingFASTA=setdiff(KOModel.rxns,[fastaFiles;alignedFiles;hmmFiles;outFiles]);
-0557 
-0558 if ~isempty(missingFASTA)
-0559     if ~exist(fullfile(dataDir,'keggdb','genes.pep'),'file')
-0560         EM=['The file ''genes.pep'' cannot be located at ' strrep(dataDir,'\','/') '/ and should be downloaded from the KEGG FTP.\n'];
-0561         dispEM(EM);
-0562     end
-0563     %Only construct models for KOs which don't have files already
-0564     fastaModel=removeReactions(KOModel,setdiff(KOModel.rxns,missingFASTA),true,true);
-0565     %Permute the order of the KOs in the model so that constructMultiFasta
-0566     %can be run on several processors at once
-0567     fastaModel=permuteModel(fastaModel,randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(fastaModel.rxns)),'rxns');
-0568     constructMultiFasta(fastaModel,fullfile(dataDir,'keggdb','genes.pep'),fullfile(dataDir,'fasta'));
-0569 else
-0570     fprintf('Generating the KEGG Orthology specific multi-FASTA files... COMPLETE\n');
-0571 end
-0572 
-0573 if isunix
-0574     if ismac
-0575         binEnd='.mac';
-0576     else
-0577         binEnd='';
-0578     end
-0579 elseif ispc
-0580     binEnd='';
-0581 else
-0582     EM='Unknown OS, exiting.';
-0583     disp(EM);
-0584     return
-0585 end
-0586 
-0587 %Check if alignment of FASTA files should be performed
-0588 missingAligned=setdiff(KOModel.rxns,[alignedFiles;hmmFiles;alignedWorking;outFiles]);
-0589 if ~isempty(missingAligned)
-0590     if seqIdentity==-1
-0591         fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets... ');
-0592     else
-0593         fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets... ');
-0594     end
-0595     missingAligned=missingAligned(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingAligned)));
-0596     progressFlag=0;
-0597     %Update fastaFiles. This is needed once rebuilding KEGG from FTP dump
-0598     %files for more accurate progress reporting
-0599     fastaFiles=listFiles(fullfile(dataDir,'fasta','*.fa'));
-0600     %Align all sequences using MAFFT
-0601     for i=1:numel(missingAligned)
-0602         %This is checked here because it could be that it is created by a
-0603         %parallel process. The faw-files are saved as temporary files to
-0604         %kept track of which files are being worked on
-0605         if ~exist(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'file') &&...
-0606                 ~exist(fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'file')
-0607             %Check that the multi-FASTA file exists. It should do so since
-0608             %we are saving empty files as well. Print a warning and
-0609             %continue if not
-0610             if ~exist(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']),'file')
-0611                 EM=['WARNING: The multi-FASTA file for ' missingAligned{i} ' does not exist'];
-0612                 dispEM(EM,false);
-0613                 continue;
-0614             end
-0615             
-0616             %If the multi-FASTA file is empty then save an empty aligned
-0617             %file and continue
-0618             s=dir(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']));
-0619             if s.bytes<=0
-0620                 fid=fopen(fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'w');
-0621                 fclose(fid);
-0622                 continue;
-0623             end
-0624             
-0625             %Create an empty file to prevent other threads to start to work
-0626             %on the same alignment
-0627             fid=fopen(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'w');
-0628             fclose(fid);
-0629             
-0630             %First load the FASTA file, then select up to nSequences
-0631             %sequences of the most closely related species, apply any
-0632             %constraints from maxPhylDist, and save it as a temporary file,
-0633             %and create the model from that
+0534 if ~isempty(missingFASTA)
+0535     if ~exist(fullfile(dataDir,'keggdb','genes.pep'),'file')
+0536         EM=['The file ''genes.pep'' cannot be located at ' strrep(dataDir,'\','/') '/ and should be downloaded from the KEGG FTP.\n'];
+0537         dispEM(EM);
+0538     end
+0539     %Only construct models for KOs which don't have files already
+0540     fastaModel=removeReactions(KOModel,setdiff(KOModel.rxns,missingFASTA),true,true);
+0541     %Permute the order of the KOs in the model so that constructMultiFasta
+0542     %can be run on several processors at once
+0543     fastaModel=permuteModel(fastaModel,randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(fastaModel.rxns)),'rxns');
+0544     constructMultiFasta(fastaModel,fullfile(dataDir,'keggdb','genes.pep'),fullfile(dataDir,'fasta'));
+0545 else
+0546     fprintf('Generating the KEGG Orthology specific multi-FASTA files... COMPLETE\n');
+0547 end
+0548 
+0549 if isunix
+0550     if ismac
+0551         binEnd='.mac';
+0552     else
+0553         binEnd='';
+0554     end
+0555 elseif ispc
+0556     binEnd='';
+0557 else
+0558     EM='Unknown OS, exiting.';
+0559     disp(EM);
+0560     return
+0561 end
+0562 
+0563 %Check if alignment of FASTA files should be performed
+0564 missingAligned=setdiff(KOModel.rxns,[alignedFiles;hmmFiles;alignedWorking;outFiles]);
+0565 if ~isempty(missingAligned)
+0566     if seqIdentity==-1
+0567         fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets...   0%% complete');
+0568     else
+0569         fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets...   0%% complete');
+0570     end
+0571     missingAligned=missingAligned(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingAligned)));
+0572     tmpFile=tempname;
+0573     %On Windows, paths need to be translated to Unix before parsing it to WSL
+0574     if ispc
+0575         wslPath.tmpFile=getWSLpath(tmpFile);
+0576         %mafft has problems writing to terminal (/dev/stderr) when running
+0577         %on WSL via MATLAB, instead write and read progress file
+0578         mafftOutput = tempname;
+0579         wslPath.mafftOutput=getWSLpath(mafftOutput);
+0580         wslPath.mafft=getWSLpath(fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat'));
+0581         wslPath.cdhit=getWSLpath(fullfile(ravenPath,'software','cd-hit','cd-hit'));
+0582     end
+0583     
+0584     for i=1:numel(missingAligned)
+0585         %This is checked here because it could be that it is created by a
+0586         %parallel process. The faw-files are saved as temporary files to
+0587         %kept track of which files are being worked on
+0588         if ~exist(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'file') &&...
+0589                 ~exist(fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'file')
+0590             %Check that the multi-FASTA file exists. It should do so since
+0591             %we are saving empty files as well. Print a warning and
+0592             %continue if not
+0593             if ~exist(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']),'file')
+0594                 EM=['WARNING: The multi-FASTA file for ' missingAligned{i} ' does not exist'];
+0595                 dispEM(EM,false);
+0596                 continue;
+0597             end
+0598             
+0599             %If the multi-FASTA file is empty then save an empty aligned
+0600             %file and continue
+0601             s=dir(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']));
+0602             if s.bytes<=0
+0603                 fid=fopen(fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'w');
+0604                 fclose(fid);
+0605                 continue;
+0606             end
+0607             
+0608             %Create an empty file to prevent other threads to start to work
+0609             %on the same alignment
+0610             fid=fopen(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'w');
+0611             fclose(fid);
+0612             
+0613             %First load the FASTA file, then select up to nSequences
+0614             %sequences of the most closely related species, apply any
+0615             %constraints from maxPhylDist, and save it as a temporary file,
+0616             %and create the model from that
+0617             
+0618             fastaStruct=fastaread(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']));
+0619             phylDist=inf(numel(fastaStruct),1);
+0620             for j=1:numel(fastaStruct)
+0621                 %Get the organism abbreviation
+0622                 index=strfind(fastaStruct(j).Header,':');
+0623                 if any(index)
+0624                     abbrev=fastaStruct(j).Header(1:index(1)-1);
+0625                     [~, index]=ismember(abbrev,phylDistStruct.ids);
+0626                     if any(index)
+0627                         phylDist(j)=phylDistStruct.distMat(index(1),phylDistId);
+0628                     end
+0629                 end
+0630             end
+0631             
+0632             %Inf means that it should not be included
+0633             phylDist(phylDist>maxPhylDist)=[];
 0634             
-0635             fastaStruct=fastaread(fullfile(dataDir,'fasta',[missingAligned{i} '.fa']));
-0636             phylDist=inf(numel(fastaStruct),1);
-0637             for j=1:numel(fastaStruct)
-0638                 %Get the organism abbreviation
-0639                 index=strfind(fastaStruct(j).Header,':');
-0640                 if any(index)
-0641                     abbrev=fastaStruct(j).Header(1:index(1)-1);
-0642                     [~, index]=ismember(abbrev,phylDistStruct.ids);
-0643                     if any(index)
-0644                         phylDist(j)=phylDistStruct.distMat(index(1),phylDistId);
-0645                     end
-0646                 end
-0647             end
-0648             
-0649             %Inf means that it should not be included
-0650             phylDist(phylDist>maxPhylDist)=[];
-0651             
-0652             %Sort based on phylDist
-0653             [~, order]=sort(phylDist);
-0654             
-0655             %Save the first nSequences hits to a temporary FASTA file
-0656             if nSequences<=numel(fastaStruct)
-0657                 fastaStruct=fastaStruct(order(1:nSequences));
-0658             else
-0659                 fastaStruct=fastaStruct(order);
-0660             end
-0661             
-0662             %Do the clustering and alignment if there are more than one
-0663             %sequences, otherwise just save the sequence (or an empty file)
-0664             if numel(fastaStruct)>1
-0665                 if seqIdentity==0.9
-0666                     cdhitInp100=tempname;
-0667                     fastawrite(cdhitInp100,fastaStruct);
-0668                     cdhitInp90=tempname;
-0669                     [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
-0670                     if status~=0
-0671                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0672                         dispEM(EM);
-0673                     end
-0674                     %Remove the old tempfile
-0675                     if exist(cdhitInp100, 'file')
-0676                         delete([cdhitInp100 '*']);
-0677                     end
-0678                     tmpFile=tempname;
-0679                     [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' tmpFile '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
-0680                     if status~=0
-0681                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0682                         dispEM(EM);
-0683                     end
-0684                     %Remove the old tempfile
-0685                     if exist(cdhitInp90, 'file')
-0686                         delete([cdhitInp90 '*']);
-0687                     end
-0688                 elseif seqIdentity==0.5
-0689                     cdhitInp100=tempname;
-0690                     fastawrite(cdhitInp100,fastaStruct);
-0691                     cdhitInp90=tempname;
-0692                     [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
-0693                     if status~=0
-0694                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0695                         dispEM(EM);
-0696                     end
-0697                     %Remove the old tempfile
-0698                     if exist(cdhitInp100, 'file')
-0699                         delete([cdhitInp100 '*']);
-0700                     end
-0701                     cdhitInp50=tempname;
-0702                     [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' cdhitInp50 '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
-0703                     if status~=0
-0704                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0705                         dispEM(EM);
-0706                     end
-0707                     %Remove the old tempfile
-0708                     if exist(cdhitInp90, 'file')
-0709                         delete([cdhitInp90 '*']);
-0710                     end
-0711                     tmpFile=tempname;
-0712                     [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp50 '" -o "' tmpFile '" -c 0.5 -n 3 -M 2000 -aL 0.8']);
-0713                     if status~=0
-0714                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0715                         dispEM(EM);
-0716                     end
-0717                     %Remove the old tempfile
-0718                     if exist(cdhitInp50, 'file')
-0719                         delete([cdhitInp50 '*']);
-0720                     end
-0721                 elseif seqIdentity~=-1
-0722                     cdhitInpCustom=tempname;
-0723                     fastawrite(cdhitInpCustom,fastaStruct);
-0724                     tmpFile=tempname;
-0725                     if seqIdentity<=1 && seqIdentity>0.7
-0726                         [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 5 -M 2000']);
-0727                     elseif seqIdentity>0.6
-0728                         [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 4 -M 2000']);
-0729                     elseif seqidentity>0.5
-0730                         [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 3 -M 2000']);
-0731                     elseif seqidentity>0.4
-0732                         [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 2 -M 2000']);
-0733                     else
-0734                         EM='The provided seqIdentity must be between 0 and 1\n';
-0735                         dispEM(EM);
-0736                     end
-0737                     if status~=0
-0738                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-0739                         dispEM(EM);
-0740                     end
-0741                     %Remove the old tempfile
-0742                     if exist(cdhitInpCustom, 'file')
-0743                         delete([cdhitInpCustom '*']);
-0744                     end
-0745                 else
-0746                     %This means that CD-HIT should be skipped since
-0747                     %seqIdentity is equal to -1
-0748                     tmpFile=tempname;
-0749                     fastawrite(tmpFile,fastaStruct);
-0750                 end
-0751                 %Do the alignment for this file
-0752                 if ismac
-0753                     [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-mac','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
-0754                 elseif isunix
-0755                     [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
-0756                 elseif ispc
-0757                     [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-win','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
-0758                 end
-0759                 if status~=0
-0760                     %It could be that alignment failed because only one
-0761                     %sequence was left after clustering. If that is the
-0762                     %case, then the clustered file is just copied as 'faw'
-0763                     %file
-0764                     if any(regexp(output,'Only 1 sequence found'))
-0765                         movefile(tmpFile,fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'f');
-0766                     else
-0767                         EM=['Error when performing alignment of ' missingAligned{i} ':\n' output];
-0768                         dispEM(EM);
-0769                     end
-0770                 end
-0771                 %Remove the old tempfile
-0772                 if exist(tmpFile, 'file')
-0773                     delete([tmpFile '*']);
-0774                 end
-0775             else
-0776                 %If there is only one sequence then it's not possible to do
-0777                 %a multiple alignment. Just print the sequence instead. An
-0778                 %empty file was written previously so that doesn't have to
-0779                 %be dealt with
-0780                 if numel(fastaStruct)==1
-0781                     fastawrite(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fastaStruct);
-0782                 end
-0783             end
-0784             %Move the temporary file to the real one
-0785             movefile(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'f');
-0786             
-0787             %Print the progress: no need to update this for every
-0788             %iteration, just report once 25%, 50% and 75% are done
-0789             if progressFlag==0 && i>numel(missingAligned)*0.25
-0790                 fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.fa')))/numel(fastaFiles))*100);
-0791                 progressFlag=progressFlag+1;
-0792             elseif (progressFlag==1 && i>=numel(missingAligned)*0.5) || (progressFlag==2 && i>=numel(missingAligned)*0.75)
-0793                 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.fa')))/numel(fastaFiles))*100);
-0794                 progressFlag=progressFlag+1;
-0795             end
-0796         end
-0797     end
-0798     fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
-0799 else
-0800     if seqIdentity==-1
-0801         fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets... COMPLETE\n');
-0802     else
-0803         fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets... COMPLETE\n');
-0804     end
-0805 end
-0806 
-0807 %Check if training of Hidden Markov models should be performed
-0808 missingHMMs=setdiff(KOModel.rxns,[hmmFiles;outFiles]);
-0809 if ~isempty(missingHMMs)
-0810     fprintf('Training the KEGG Orthology specific HMMs... ');
-0811     missingHMMs=missingHMMs(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingHMMs)));
-0812     progressFlag=0;
-0813     %Update alignedFiles. This is needed once rebuilding KEGG from FTP dump
-0814     %files for more accurate progress reporting
-0815     alignedFiles=listFiles(fullfile(dataDir,'aligned','*.fa'));
-0816     %Train models for all missing KOs
-0817     for i=1:numel(missingHMMs)
-0818         %This is checked here because it could be that it is created by a
-0819         %parallel process
-0820         if ~exist(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']),'file') && ~exist(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']),'file')
-0821             %Check that the aligned FASTA file exists. It could be that it
-0822             %is still being worked on by some other instance of the program
-0823             %(the .faw file should then exist). This should not happen on a
-0824             %single computer. It doesn't throw an error, because it should
-0825             %finalize the ones it can
-0826             if ~exist(fullfile(dataDir,'aligned',[missingHMMs{i} '.fa']),'file')
-0827                 EM=['The aligned FASTA file for ' missingHMMs{i} ' does not exist'];
-0828                 dispEM(EM,false);
-0829                 continue;
-0830             end
-0831             
-0832             %If the multi-FASTA file is empty then save an empty aligned
-0833             %file and continue
-0834             s=dir(fullfile(dataDir,'aligned',[missingHMMs{i} '.fa']));
-0835             if s.bytes<=0
-0836                 fid=fopen(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']),'w');
-0837                 fclose(fid);
-0838                 continue;
-0839             end
-0840             %Create a temporary file to indicate that it is working on the
-0841             %KO. This is because hmmbuild cannot overwrite existing files
-0842             fid=fopen(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']),'w');
-0843             fclose(fid);
-0844             
-0845             %Create HMM
-0846             [status, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmbuild' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']) '" "' fullfile(dataDir,'aligned',[missingHMMs{i} '.fa']) '"']);
-0847             if status~=0
-0848                 EM=['Error when training HMM for ' missingHMMs{i} ':\n' output];
-0849                 dispEM(EM);
-0850             end
-0851             
-0852             %Delete the temporary file
-0853             delete(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']));
-0854             
-0855             %Print the progress: no need to update this for every
-0856             %iteration, just report once 25%, 50% and 75% are done
-0857             if progressFlag==0 && i>numel(missingHMMs)*0.25
-0858                 fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.hmm')))/numel(alignedFiles))*100);
-0859                 progressFlag=progressFlag+1;
-0860             elseif (progressFlag==1 && i>=numel(missingHMMs)*0.5) || (progressFlag==2 && i>=numel(missingHMMs)*0.75)
-0861                 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.hmm')))/numel(alignedFiles))*100);
-0862                 progressFlag=progressFlag+1;
-0863             end
-0864         end
-0865     end
-0866     fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
-0867 else
-0868     fprintf('Training the KEGG Orthology specific HMMs... COMPLETE\n');
-0869 end
-0870 
-0871 %Check which new .out files that should be generated. Check if training of
-0872 %Hidden Markov models should be performed
-0873 missingOUT=setdiff(KOModel.rxns,outFiles);
-0874 if ~isempty(missingOUT)
-0875     fprintf(['Querying <strong>' strrep(fastaFile,'\','/') '</strong> against the KEGG Orthology specific HMMs... ']);
-0876     missingOUT=missingOUT(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingOUT)));
-0877     progressFlag=0;
-0878     %Update hmmFiles. This is needed once rebuilding KEGG from FTP dump
-0879     %files for more accurate progress reporting
-0880     hmmFiles=listFiles(fullfile(dataDir,'hmms','*.hmm'));
-0881     for i=1:numel(missingOUT)
-0882         %This is checked here because it could be that it is created by a
-0883         %parallel process
-0884         if ~exist(fullfile(outDir,[missingOUT{i} '.out']),'file')
-0885             %Check that the HMM file exists. It should do so since %we are
-0886             %saving empty files as well. Print a warning and continue if
-0887             %not
-0888             if ~exist(fullfile(dataDir,'hmms',[missingOUT{i} '.hmm']),'file')
-0889                 EM=['The HMM file for ' missingOUT{i} ' does not exist'];
-0890                 dispEM(EM,false);
-0891                 continue;
-0892             end
-0893             
-0894             %Save an empty file to prevent several threads working on the
-0895             %same file
-0896             fid=fopen(fullfile(outDir,[missingOUT{i} '.out']),'w');
-0897             fclose(fid);
-0898             
-0899             %If the HMM file is empty then save an out file and continue
-0900             s=dir(fullfile(dataDir,'hmms',[missingOUT{i} '.hmm']));
-0901             if s.bytes<=0
-0902                 continue;
-0903             end
-0904             
-0905             %Check each gene in the input file against this model
-0906             [status, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(dataDir,'hmms',[missingOUT{i} '.hmm']) '" "' fastaFile '"']);
-0907             if status~=0
-0908                 EM=['Error when querying HMM for ' missingOUT{i} ':\n' output];
-0909                 dispEM(EM);
-0910             end
-0911             
-0912             %Save the output to a file
-0913             fid=fopen(fullfile(outDir,[missingOUT{i} '.out']),'w');
-0914             fwrite(fid,output);
-0915             fclose(fid);
-0916             
-0917             %Print the progress: no need to update this for every
-0918             %iteration, just report once 25%, 50% and 75% are done
-0919             if progressFlag==0 && i>numel(missingOUT)*0.25
-0920                 fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(outDir,'*.out')))/numel(hmmFiles))*100);
-0921                 progressFlag=progressFlag+1;
-0922             elseif (progressFlag==1 && i>=numel(missingOUT)*0.5) || (progressFlag==2 && i>=numel(missingOUT)*0.75)
-0923                 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(outDir,'*.out')))/numel(hmmFiles))*100);
-0924                 progressFlag=progressFlag+1;
-0925             end
-0926         end
-0927     end
-0928     fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
-0929 else
-0930     fprintf(['Querying <strong>' fastaFile '</strong> against the KEGG Orthology specific HMMs... COMPLETE\n']);
-0931 end
-0932 
-0933 
-0934 %***Begin retrieving the output and putting together the resulting model
-0935 
-0936 fprintf('Parsing the HMM search results... ');
-0937 %Retrieve matched genes from the HMMs
-0938 koGeneMat=zeros(numel(KOModel.rxns),3000); %Make room for 3000 genes
-0939 genes=cell(3000,1);
-0940 %Store the best score for a gene in a hash list (since it will be searching
-0941 %many times)
-0942 hTable = java.util.Hashtable;
-0943 
-0944 geneCounter=0;
-0945 for i=1:numel(KOModel.rxns)
-0946     if exist(fullfile(outDir,[KOModel.rxns{i} '.out']), 'file')
-0947         fid=fopen(fullfile(outDir,[KOModel.rxns{i} '.out']),'r');
-0948         beginMatches=false;
-0949         while 1
-0950             %Get the next line
-0951             tline = fgetl(fid);
-0952             
-0953             %Abort at end of file
-0954             if ~ischar(tline)
-0955                 break;
-0956             end
-0957             
-0958             if and(beginMatches,strcmp(tline,'  ------ inclusion threshold ------'))
-0959                 break;
-0960             end
-0961             
-0962             if beginMatches==false
-0963                 %This is how the listing of matches begins
-0964                 if any(strfind(tline,'E-value '))
-0965                     %Read one more line that is only padding
-0966                     tline = fgetl(fid);
-0967                     beginMatches=true;
-0968                 end
-0969             else
-0970                 %If matches should be read
-0971                 if ~strcmp(tline,'   [No hits detected that satisfy reporting thresholds]') && ~isempty(tline)
-0972                     elements=regexp(tline,' ','split');
-0973                     elements=elements(cellfun(@any,elements));
-0974                     
-0975                     %Check if the match is below the treshhold
-0976                     score=str2double(elements{1});
-0977                     gene=elements{9};
-0978                     if score<=cutOff
-0979                         %If the score is exactly 0, change it to a very
-0980                         %small value to avoid NaN
-0981                         if score==0
-0982                             score=10^-250;
-0983                         end
-0984                         %Check if the gene is added already and, is so, get
-0985                         %the best score for it
-0986                         I=hTable.get(gene);
-0987                         if any(I)
-0988                             koGeneMat(i,I)=score;
-0989                         else
-0990                             geneCounter=geneCounter+1;
-0991                             %The gene was not present yet so add it
-0992                             hTable.put(gene,geneCounter);
-0993                             genes{geneCounter}=gene;
-0994                             koGeneMat(i,geneCounter)=score;
-0995                         end
-0996                     end
-0997                 else
-0998                     break;
-0999                 end
-1000             end
-1001         end
-1002         fclose(fid);
-1003     end
-1004 end
-1005 fprintf('COMPLETE\n');
-1006 
-1007 fprintf('Removing gene, KEGG Orthology associations below minScoreRatioKO, minScoreRatioG... ');
-1008 koGeneMat=koGeneMat(:,1:geneCounter);
-1009 
-1010 %Remove the genes for each KO that are below minScoreRatioKO.
-1011 for i=1:size(koGeneMat,1)
-1012     J=find(koGeneMat(i,:));
-1013     if any(J)
-1014         koGeneMat(i,J(log(koGeneMat(i,J))/log(min(koGeneMat(i,J)))<minScoreRatioKO))=0;
-1015     end
-1016 end
-1017 
-1018 %Remove the KOs for each gene that are below minScoreRatioG
-1019 for i=1:size(koGeneMat,2)
-1020     J=find(koGeneMat(:,i));
-1021     if any(J)
-1022         koGeneMat(J(log(koGeneMat(J,i))/log(min(koGeneMat(J,i)))<minScoreRatioG),i)=0;
-1023     end
-1024 end
-1025 fprintf('COMPLETE\n');
-1026 
-1027 fprintf('Adding gene annotations to the model... ');
-1028 %Create the new model
-1029 model.genes=genes(1:geneCounter);
-1030 model.grRules=cell(numel(model.rxns),1);
-1031 model.grRules(:)={''};
-1032 model.rxnGeneMat=sparse(numel(model.rxns),numel(model.genes));
-1033 
-1034 %Loop through the reactions and add the corresponding genes
-1035 for i=1:numel(model.rxns)
-1036     if isstruct(model.rxnMiriams{i})
-1037         %Get all KOs
-1038         I=find(strcmpi(model.rxnMiriams{i}.name,'kegg.orthology'));
-1039         KOs=model.rxnMiriams{i}.value(I);
-1040         %Find the KOs and the corresponding genes
-1041         J=ismember(KOModel.rxns,KOs);
-1042         [~, K]=find(koGeneMat(J,:));
-1043         
-1044         if any(K)
-1045             model.rxnGeneMat(i,K)=1;
-1046             %Also delete KOs for which no genes were found. If no genes at
-1047             %all were matched to the reaction it will be deleted later
-1048             L=sum(koGeneMat(J,:),2)==0;
-1049             model.rxnMiriams{i}.value(I(L))=[];
-1050             model.rxnMiriams{i}.name(I(L))=[];
-1051         end
-1052     end
-1053 end
-1054 fprintf('COMPLETE\n');
-1055 
-1056 %Find and delete all reactions without genes. This also removes genes that
-1057 %are not used (which could happen because minScoreRatioG and
-1058 %minScoreRatioKO). If keepSpontaneous==true, the spontaneous reactions
-1059 %without genes are kept in the model. Spontaneous reactions with original
-1060 %gene associations are treated in the same way, like the rest of the
-1061 %reactions - if gene associations were removed during HMM search, such
-1062 %reactions are deleted from the model
-1063 if keepSpontaneous==true
-1064     %Not the most comprise way to delete reactions without genes, but this
-1065     %makes the code easier to understand. Firstly the non-spontaneous
-1066     %reactions without genes are removed. After that, the second deletion
-1067     %step removes spontaneous reactions, which had gene associations before
-1068     %HMM search, but no longer have after it
-1069     fprintf('Removing non-spontaneous reactions which after HMM search no longer have GPR rules... ');
-1070     I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous);
-1071     model=removeReactions(model,I,true,true);
-1072     I=~any(model.rxnGeneMat,2)&ismember(model.rxns,spontRxnsWithGenes);
-1073     model=removeReactions(model,I,true,true);
-1074 else
-1075     %Just simply check for any new reactions without genes and remove
-1076     %it
-1077     fprintf('Removing reactions which after HMM search no longer have GPR rules... ');
-1078     I=~any(model.rxnGeneMat,2);
-1079     model=removeReactions(model,I,true,true);
-1080 end
-1081 fprintf('COMPLETE\n');
-1082 
-1083 fprintf('Constructing GPR rules and finalizing the model... ');
-1084 %Add the gene associations as 'or'
-1085 for i=1:numel(model.rxns)
-1086     %Find the involved genes
-1087     I=find(model.rxnGeneMat(i,:));
-1088     if any(I)
-1089         model.grRules{i}=['(' model.genes{I(1)}];
-1090         for j=2:numel(I)
-1091             model.grRules{i}=[model.grRules{i} ' or ' model.genes{I(j)}];
-1092         end
-1093         model.grRules{i}=[model.grRules{i} ')'];
-1094     end
-1095 end
-1096 
-1097 %Fix grRules and reconstruct rxnGeneMat
-1098 [grRules,rxnGeneMat] = standardizeGrRules(model,false); %Give detailed output
-1099 model.grRules = grRules;
-1100 model.rxnGeneMat = rxnGeneMat;
-1101 
-1102 %Add the description to the reactions
-1103 for i=1:numel(model.rxns)
-1104     if ~isempty(model.rxnNotes{i})
-1105         model.rxnNotes(i)=strcat('Included by getKEGGModelForOrganism (using HMMs).',model.rxnNotes(i));
-1106         model.rxnNotes(i)=strrep(model.rxnNotes(i),'.','. ');
-1107     else
-1108         model.rxnNotes(i)={'Included by getKEGGModelForOrganism (using HMMs)'};
-1109     end
-1110 end
-1111 fprintf('COMPLETE\n\n*** Model reconstruction complete ***\n');
-1112 end
-1113 
-1114 function files=listFiles(directory)
-1115 %Supporter function to list the files in a directory and return them as a
-1116 %cell array
-1117 temp=dir(directory);
-1118 files=cell(numel(temp),1);
-1119 for i=1:numel(temp)
-1120     files{i}=temp(i,1).name;
-1121 end
-1122 files=strrep(files,'.fa','');
-1123 files=strrep(files,'.hmm','');
-1124 files=strrep(files,'.out','');
-1125 files=strrep(files,'.faw','');
-1126 end
    +0635 %Sort based on phylDist +0636 [~, order]=sort(phylDist); +0637 +0638 %Save the first nSequences hits to a temporary FASTA file +0639 if nSequences<=numel(fastaStruct) +0640 fastaStruct=fastaStruct(order(1:nSequences)); +0641 else +0642 fastaStruct=fastaStruct(order); +0643 end +0644 +0645 %Do the clustering and alignment if there are more than one +0646 %sequences, otherwise just save the sequence (or an empty file) +0647 if numel(fastaStruct)>1 +0648 if seqIdentity~=-1 +0649 cdhitInpCustom=tempname; +0650 fastawrite(cdhitInpCustom,fastaStruct); +0651 if seqIdentity<=1 && seqIdentity>0.7 +0652 nparam='5'; +0653 elseif seqIdentity>0.6 +0654 nparam='4'; +0655 elseif seqIdentity>0.5 +0656 nparam='3'; +0657 elseif seqIdentity>0.4 +0658 nparam='2'; +0659 else +0660 EM='The provided seqIdentity must be between 0 and 1\n'; +0661 dispEM(EM); +0662 end +0663 if ispc +0664 wslPath.cdhitInpCustom=getWSLpath(cdhitInpCustom); +0665 [status, output]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.cdhitInpCustom '" -o "' wslPath.tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']); +0666 elseif ismac || isunix +0667 [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']); +0668 end +0669 if status~=0 +0670 EM=['Error when performing clustering of ' missingAligned{i} ':\n' output]; +0671 dispEM(EM); +0672 end +0673 %Remove the old tempfile +0674 if exist(cdhitInpCustom, 'file') +0675 delete([cdhitInpCustom '*']); +0676 end +0677 else +0678 %This means that CD-HIT should be skipped since +0679 %seqIdentity is equal to -1 +0680 fastawrite(tmpFile,fastaStruct); +0681 end +0682 %Do the alignment for this file +0683 if ismac +0684 [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-mac','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']); +0685 elseif isunix +0686 [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']); +0687 elseif ispc +0688 wslPath.fawFile=getWSLpath(fullfile(dataDir,'aligned',[missingAligned{i} '.faw'])); +0689 [status, ~]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --progress "' wslPath.mafftOutput '" --thread "' num2str(cores) '" --out "' wslPath.fawFile '" "' wslPath.tmpFile '"']); +0690 output=fileread(mafftOutput); +0691 delete(mafftOutput); +0692 end +0693 if status~=0 +0694 %It could be that alignment failed because only one +0695 %sequence was left after clustering. If that is the +0696 %case, then the clustered file is just copied as 'faw' +0697 %file +0698 if any(regexp(output,'Only 1 sequence found')) +0699 movefile(tmpFile,fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),'f'); +0700 else +0701 EM=['Error when performing alignment of ' missingAligned{i} ':\n' output]; +0702 dispEM(EM); +0703 end +0704 end +0705 %Remove the old tempfile +0706 if exist(tmpFile, 'file') +0707 delete([tmpFile '*']); +0708 end +0709 else +0710 %If there is only one sequence then it's not possible to do +0711 %a multiple alignment. Just print the sequence instead. An +0712 %empty file was written previously so that doesn't have to +0713 %be dealt with +0714 if numel(fastaStruct)==1 +0715 warnState = warning; %Save the current warning state +0716 warning('off','Bioinfo:fastawrite:AppendToFile'); +0717 fastawrite(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fastaStruct); +0718 warning(warnState) %Reset warning state to previous settings +0719 end +0720 end +0721 %Move the temporary file to the real one +0722 movefile(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'f'); +0723 +0724 %Print the progress every 25 files +0725 if rem(i-1,25) == 0 +0726 progress=num2str(floor(100*numel(listFiles(fullfile(dataDir,'aligned','*.fa')))/numel(KOModel.rxns))); +0727 progress=pad(progress,3,'left'); +0728 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress); +0729 end +0730 end +0731 end +0732 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'); +0733 else +0734 if seqIdentity==-1 +0735 fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets... COMPLETE\n'); +0736 else +0737 fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets... COMPLETE\n'); +0738 end +0739 end +0740 +0741 %Check if training of Hidden Markov models should be performed +0742 missingHMMs=setdiff(KOModel.rxns,[hmmFiles;outFiles]); +0743 if ~isempty(missingHMMs) +0744 fprintf('Training the KEGG Orthology specific HMMs... 0%% complete'); +0745 missingHMMs=missingHMMs(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingHMMs))); +0746 %Train models for all missing KOs +0747 for i=1:numel(missingHMMs) +0748 %This is checked here because it could be that it is created by a +0749 %parallel process +0750 if ~exist(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']),'file') && ~exist(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']),'file') +0751 %Check that the aligned FASTA file exists. It could be that it +0752 %is still being worked on by some other instance of the program +0753 %(the .faw file should then exist). This should not happen on a +0754 %single computer. It doesn't throw an error, because it should +0755 %finalize the ones it can +0756 if ~exist(fullfile(dataDir,'aligned',[missingHMMs{i} '.fa']),'file') +0757 EM=['The aligned FASTA file for ' missingHMMs{i} ' does not exist']; +0758 dispEM(EM,false); +0759 continue; +0760 end +0761 +0762 %If the multi-FASTA file is empty then save an empty aligned +0763 %file and continue +0764 s=dir(fullfile(dataDir,'aligned',[missingHMMs{i} '.fa'])); +0765 if s.bytes<=0 +0766 fid=fopen(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']),'w'); +0767 fclose(fid); +0768 continue; +0769 end +0770 %Create a temporary file to indicate that it is working on the +0771 %KO. This is because hmmbuild cannot overwrite existing files +0772 fid=fopen(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']),'w'); +0773 fclose(fid); +0774 +0775 %Create HMM +0776 [status, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmbuild' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(dataDir,'hmms',[missingHMMs{i} '.hmm']) '" "' fullfile(dataDir,'aligned',[missingHMMs{i} '.fa']) '"']); +0777 if status~=0 +0778 EM=['Error when training HMM for ' missingHMMs{i} ':\n' output]; +0779 dispEM(EM); +0780 end +0781 +0782 %Delete the temporary file +0783 delete(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw'])); +0784 +0785 %Print the progress every 25 files +0786 if rem(i-1,25) == 0 +0787 progress=num2str(floor(100*numel(listFiles(fullfile(dataDir,'hmms','*.hmm')))/numel(KOModel.rxns))); +0788 progress=pad(progress,3,'left'); +0789 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress); +0790 end +0791 end +0792 end +0793 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'); +0794 else +0795 fprintf('Training the KEGG Orthology specific HMMs... COMPLETE\n'); +0796 end +0797 +0798 %Check which new .out files that should be generated. Check if training of +0799 %Hidden Markov models should be performed +0800 missingOUT=setdiff(KOModel.rxns,outFiles); +0801 if ~isempty(missingOUT) +0802 fprintf('Querying the user-specified FASTA file against the KEGG Orthology specific HMMs... 0%% complete'); +0803 missingOUT=missingOUT(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingOUT))); +0804 for i=1:numel(missingOUT) +0805 %This is checked here because it could be that it is created by a +0806 %parallel process +0807 if ~exist(fullfile(outDir,[missingOUT{i} '.out']),'file') +0808 %Check that the HMM file exists. It should do so since %we are +0809 %saving empty files as well. Print a warning and continue if +0810 %not +0811 if ~exist(fullfile(dataDir,'hmms',[missingOUT{i} '.hmm']),'file') +0812 EM=['The HMM file for ' missingOUT{i} ' does not exist']; +0813 dispEM(EM,false); +0814 continue; +0815 end +0816 +0817 %Save an empty file to prevent several threads working on the +0818 %same file +0819 fid=fopen(fullfile(outDir,[missingOUT{i} '.out']),'w'); +0820 fclose(fid); +0821 +0822 %If the HMM file is empty then save an out file and continue +0823 s=dir(fullfile(dataDir,'hmms',[missingOUT{i} '.hmm'])); +0824 if s.bytes<=0 +0825 continue; +0826 end +0827 +0828 %Check each gene in the input file against this model +0829 [status, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(dataDir,'hmms',[missingOUT{i} '.hmm']) '" "' fastaFile '"']); +0830 if status~=0 +0831 EM=['Error when querying HMM for ' missingOUT{i} ':\n' output]; +0832 dispEM(EM); +0833 end +0834 +0835 %Save the output to a file +0836 fid=fopen(fullfile(outDir,[missingOUT{i} '.out']),'w'); +0837 fwrite(fid,output); +0838 fclose(fid); +0839 +0840 %Print the progress every 25 files +0841 if rem(i-1,25) == 0 +0842 progress=num2str(floor(100*numel(listFiles(fullfile(outDir,'*.out')))/numel(KOModel.rxns))); +0843 progress=pad(progress,3,'left'); +0844 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress); +0845 end +0846 end +0847 end +0848 fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'); +0849 else +0850 fprintf('Querying the user-specified FASTA file against the KEGG Orthology specific HMMs... COMPLETE\n'); +0851 end +0852 +0853 +0854 %***Begin retrieving the output and putting together the resulting model +0855 +0856 fprintf('Parsing the HMM search results... '); +0857 %Retrieve matched genes from the HMMs +0858 koGeneMat=zeros(numel(KOModel.rxns),3000); %Make room for 3000 genes +0859 genes=cell(3000,1); +0860 %Store the best score for a gene in a hash list (since it will be searching +0861 %many times) +0862 hTable = java.util.Hashtable; +0863 +0864 geneCounter=0; +0865 for i=1:numel(KOModel.rxns) +0866 if exist(fullfile(outDir,[KOModel.rxns{i} '.out']), 'file') +0867 fid=fopen(fullfile(outDir,[KOModel.rxns{i} '.out']),'r'); +0868 beginMatches=false; +0869 while 1 +0870 %Get the next line +0871 tline = fgetl(fid); +0872 +0873 %Abort at end of file +0874 if ~ischar(tline) +0875 break; +0876 end +0877 +0878 if and(beginMatches,strcmp(tline,' ------ inclusion threshold ------')) +0879 break; +0880 end +0881 +0882 if beginMatches==false +0883 %This is how the listing of matches begins +0884 if any(strfind(tline,'E-value ')) +0885 %Read one more line that is only padding +0886 tline = fgetl(fid); +0887 beginMatches=true; +0888 end +0889 else +0890 %If matches should be read +0891 if ~strcmp(tline,' [No hits detected that satisfy reporting thresholds]') && ~isempty(tline) +0892 elements=regexp(tline,' ','split'); +0893 elements=elements(cellfun(@any,elements)); +0894 +0895 %Check if the match is below the treshhold +0896 score=str2double(elements{1}); +0897 gene=elements{9}; +0898 if score<=cutOff +0899 %If the score is exactly 0, change it to a very +0900 %small value to avoid NaN +0901 if score==0 +0902 score=10^-250; +0903 end +0904 %Check if the gene is added already and, is so, get +0905 %the best score for it +0906 I=hTable.get(gene); +0907 if any(I) +0908 koGeneMat(i,I)=score; +0909 else +0910 geneCounter=geneCounter+1; +0911 %The gene was not present yet so add it +0912 hTable.put(gene,geneCounter); +0913 genes{geneCounter}=gene; +0914 koGeneMat(i,geneCounter)=score; +0915 end +0916 end +0917 else +0918 break; +0919 end +0920 end +0921 end +0922 fclose(fid); +0923 end +0924 end +0925 fprintf('COMPLETE\n'); +0926 +0927 fprintf('Removing gene, KEGG Orthology associations below minScoreRatioKO, minScoreRatioG... '); +0928 koGeneMat=koGeneMat(:,1:geneCounter); +0929 +0930 %Remove the genes for each KO that are below minScoreRatioKO. +0931 for i=1:size(koGeneMat,1) +0932 J=find(koGeneMat(i,:)); +0933 if any(J) +0934 koGeneMat(i,J(log(koGeneMat(i,J))/log(min(koGeneMat(i,J)))<minScoreRatioKO))=0; +0935 end +0936 end +0937 +0938 %Remove the KOs for each gene that are below minScoreRatioG +0939 for i=1:size(koGeneMat,2) +0940 J=find(koGeneMat(:,i)); +0941 if any(J) +0942 koGeneMat(J(log(koGeneMat(J,i))/log(min(koGeneMat(J,i)))<minScoreRatioG),i)=0; +0943 end +0944 end +0945 fprintf('COMPLETE\n'); +0946 +0947 fprintf('Adding gene annotations to the model... '); +0948 %Create the new model +0949 model.genes=genes(1:geneCounter); +0950 model.grRules=cell(numel(model.rxns),1); +0951 model.grRules(:)={''}; +0952 model.rxnGeneMat=sparse(numel(model.rxns),numel(model.genes)); +0953 +0954 %Loop through the reactions and add the corresponding genes +0955 for i=1:numel(model.rxns) +0956 if isstruct(model.rxnMiriams{i}) +0957 %Get all KOs +0958 I=find(strcmpi(model.rxnMiriams{i}.name,'kegg.orthology')); +0959 KOs=model.rxnMiriams{i}.value(I); +0960 %Find the KOs and the corresponding genes +0961 J=ismember(KOModel.rxns,KOs); +0962 [~, K]=find(koGeneMat(J,:)); +0963 +0964 if any(K) +0965 model.rxnGeneMat(i,K)=1; +0966 %Also delete KOs for which no genes were found. If no genes at +0967 %all were matched to the reaction it will be deleted later +0968 L=sum(koGeneMat(J,:),2)==0; +0969 model.rxnMiriams{i}.value(I(L))=[]; +0970 model.rxnMiriams{i}.name(I(L))=[]; +0971 end +0972 end +0973 end +0974 fprintf('COMPLETE\n'); +0975 +0976 %Find and delete all reactions without genes. This also removes genes that +0977 %are not used (which could happen because minScoreRatioG and +0978 %minScoreRatioKO). If keepSpontaneous==true, the spontaneous reactions +0979 %without genes are kept in the model. Spontaneous reactions with original +0980 %gene associations are treated in the same way, like the rest of the +0981 %reactions - if gene associations were removed during HMM search, such +0982 %reactions are deleted from the model +0983 if keepSpontaneous==true +0984 %Not the most comprise way to delete reactions without genes, but this +0985 %makes the code easier to understand. Firstly the non-spontaneous +0986 %reactions without genes are removed. After that, the second deletion +0987 %step removes spontaneous reactions, which had gene associations before +0988 %HMM search, but no longer have after it +0989 fprintf('Removing non-spontaneous reactions which after HMM search no longer have GPR rules... '); +0990 I=~any(model.rxnGeneMat,2)&~ismember(model.rxns,isSpontaneous); +0991 model=removeReactions(model,I,true,true); +0992 I=~any(model.rxnGeneMat,2)&ismember(model.rxns,spontRxnsWithGenes); +0993 model=removeReactions(model,I,true,true); +0994 else +0995 %Just simply check for any new reactions without genes and remove +0996 %it +0997 fprintf('Removing reactions which after HMM search no longer have GPR rules... '); +0998 I=~any(model.rxnGeneMat,2); +0999 model=removeReactions(model,I,true,true); +1000 end +1001 fprintf('COMPLETE\n'); +1002 +1003 fprintf('Constructing GPR rules and finalizing the model... '); +1004 %Add the gene associations as 'or' +1005 for i=1:numel(model.rxns) +1006 %Find the involved genes +1007 I=find(model.rxnGeneMat(i,:)); +1008 if any(I) +1009 model.grRules{i}=['(' model.genes{I(1)}]; +1010 for j=2:numel(I) +1011 model.grRules{i}=[model.grRules{i} ' or ' model.genes{I(j)}]; +1012 end +1013 model.grRules{i}=[model.grRules{i} ')']; +1014 end +1015 end +1016 +1017 %Fix grRules and reconstruct rxnGeneMat +1018 [grRules,rxnGeneMat] = standardizeGrRules(model,false); %Give detailed output +1019 model.grRules = grRules; +1020 model.rxnGeneMat = rxnGeneMat; +1021 +1022 %Add the description to the reactions +1023 for i=1:numel(model.rxns) +1024 if ~isempty(model.rxnNotes{i}) +1025 model.rxnNotes(i)=strcat('Included by getKEGGModelForOrganism (using HMMs).',model.rxnNotes(i)); +1026 model.rxnNotes(i)=strrep(model.rxnNotes(i),'.','. '); +1027 else +1028 model.rxnNotes(i)={'Included by getKEGGModelForOrganism (using HMMs)'}; +1029 end +1030 end +1031 %Remove the temp fasta file +1032 delete(fastaFile) +1033 fprintf('COMPLETE\n\n*** Model reconstruction complete ***\n'); +1034 end +1035 +1036 function files=listFiles(directory) +1037 %Supporter function to list the files in a directory and return them as a +1038 %cell array +1039 temp=dir(directory); +1040 files=cell(numel(temp),1); +1041 for i=1:numel(temp) +1042 files{i}=temp(i,1).name; +1043 end +1044 files=strrep(files,'.fa',''); +1045 files=strrep(files,'.hmm',''); +1046 files=strrep(files,'.out',''); +1047 files=strrep(files,'.faw',''); +1048 end
    Generated by m2html © 2005
    \ No newline at end of file diff --git a/doc/external/kegg/getModelFromKEGG.html b/doc/external/kegg/getModelFromKEGG.html index a0f5bdd5..7624e2c5 100644 --- a/doc/external/kegg/getModelFromKEGG.html +++ b/doc/external/kegg/getModelFromKEGG.html @@ -78,7 +78,7 @@

    CROSS-REFERENCE INFORMATION ^ <li><a href=getGenesFromKEGG getGenesFromKEGG
  • getMetsFromKEGG getMetsFromKEGG
  • getRxnsFromKEGG getRxnsFromKEGG
    • This function is called by: +
  • getKEGGModelForOrganism getKEGGModelForOrganism

    • SUBFUNCTIONS ^

    diff --git a/doc/external/kegg/getPhylDist.html b/doc/external/kegg/getPhylDist.html index d427a15b..3fd2bc21 100644 --- a/doc/external/kegg/getPhylDist.html +++ b/doc/external/kegg/getPhylDist.html @@ -55,7 +55,7 @@

    CROSS-REFERENCE INFORMATION ^ </ul> This function is called by: <ul style= -
  • getKEGGModelForOrganism getKEGGModelForOrganism
    • +
  • getKEGGModelForOrganism getKEGGModelForOrganism
    • diff --git a/doc/external/kegg/getWSLpath.html b/doc/external/kegg/getWSLpath.html new file mode 100644 index 00000000..b5f665d1 --- /dev/null +++ b/doc/external/kegg/getWSLpath.html @@ -0,0 +1,80 @@ + + + + Description of getWSLpath + + + + + + + + + +
    Home > external > kegg > getWSLpath.m
    + + + +

    getWSLpath +

    + +

    PURPOSE ^

    +
    getWSLpath
    + +

    SYNOPSIS ^

    +
    function path=getWSLpath(path)
    + +

    DESCRIPTION ^

    +
     getWSLpath
+   Translate Windows-style path to its Unix WSL (Windows Subsystem for
+   Linux) equivalent.
+
+   Input:
+   path        string with directory of file path, in Windows-style (e.g.
+               'C:\Directory\')
+
+   Output:
+   path        string with directory of file path, in Unix style (e.g.
+               '/mnt/c/Directory/')
+
+   Uses the WSL function 'wslpath' to translate the path.
+
+   Usage: path=getWSLpath(path)
    + + +

    CROSS-REFERENCE INFORMATION ^

    +This function calls: + +This function is called by: + + + + + +

    SOURCE CODE ^

    +
    0001 function path=getWSLpath(path)
+0002 % getWSLpath
+0003 %   Translate Windows-style path to its Unix WSL (Windows Subsystem for
+0004 %   Linux) equivalent.
+0005 %
+0006 %   Input:
+0007 %   path        string with directory of file path, in Windows-style (e.g.
+0008 %               'C:\Directory\')
+0009 %
+0010 %   Output:
+0011 %   path        string with directory of file path, in Unix style (e.g.
+0012 %               '/mnt/c/Directory/')
+0013 %
+0014 %   Uses the WSL function 'wslpath' to translate the path.
+0015 %
+0016 %   Usage: path=getWSLpath(path)
+0017 [~,path]=system(['wsl wslpath ''' path '''']);
+0018 path=path(1:end-1);% Remove final character (line-break)
+0019 end
    +
    Generated by m2html © 2005
    + + \ No newline at end of file diff --git a/doc/external/kegg/index.html b/doc/external/kegg/index.html index a6620e9d..6bb246fa 100644 --- a/doc/external/kegg/index.html +++ b/doc/external/kegg/index.html @@ -19,7 +19,7 @@

    Index for external\kegg

    Matlab files in this directory:

    -
     constructMultiFastaconstructMultiFasta
     getGenesFromKEGGgetGenesFromKEGG
     getKEGGModelForOrganismgetKEGGModelForOrganism
     getMetsFromKEGGgetMetsFromKEGG
     getModelFromKEGGgetModelFromKEGG
     getPhylDistgetPhylDist
     getRxnsFromKEGGgetRxnsFromKEGG
    + constructMultiFastaconstructMultiFasta  getGenesFromKEGGgetGenesFromKEGG  getKEGGModelForOrganismgetKEGGModelForOrganism  getMetsFromKEGGgetMetsFromKEGG  getModelFromKEGGgetModelFromKEGG  getPhylDistgetPhylDist  getRxnsFromKEGGgetRxnsFromKEGG  getWSLpathgetWSLpath

    Other Matlab-specific files in this directory:

    Matlab Files found in these Directories

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    FSEOF deleteUnusedGenes getModelFromHomology randomSampling
    SBMLFromExcel dispEM getModelFromKEGG ravenCobraWrapper
    addExchangeRxns drawMap getModelFromMetaCyc removeBadRxns
    addGenesRaven drawPathway getObjectiveString removeGenes
    addJavaPaths expandModel getPathwayDimensions removeMets
    addMets exportForGit getPhylDist removeReactions
    addRavenToUserPath exportModel getRxnsFromKEGG replaceMets
    addRxns exportModelToSIF getRxnsFromMetaCyc reporterMetabolites
    addRxnsGenesMets exportToExcelFormat getRxnsInComp runINIT
    addSpontaneousRxns exportToTabDelimited getToolboxVersion scoreModel
    addTransport extractMiriam getTransportRxns setColorToMapRxns
    analyzeSampling fillGaps getWoLFScores setExchangeBounds
    buildEquation findGeneDeletions guessComposition setOmicDataToRxns
    canConsume fitParameters gurobiToCobraRes setParam
    canProduce fitTasks haveFlux setRavenSolver
    changeGeneAssoc followChanged importExcelModel setTitle
    changeGrRules followFluxes importModel simplifyModel
    changeRxns gapReport linkMetaCycKEGGRxns solveLP
    checkFileExistence generateNewIds loadSheet solveQP
    checkFunctionUniqueness getAllRxnsFromGenes loadWorkbook sortModel
    checkInstallation getAllSubGraphs makeFakeBlastStructure standardizeGrRules
    checkModelStruct getAllowedBounds makeSomething standardizeModelFieldOrder
    checkProduction getBlast mapCompartments startup
    checkRxn getBlastFromExcel mapPathwayRxnNames testBlast
    checkSolution getColorCodes markPathwayWithExpression testDiamond
    checkTasks getDiamond markPathwayWithFluxes tinitTests
    cleanSheet getElementalBalance mergeCompartments trimPathway
    closeModel getEnzymesFromMetaCyc mergeModels tutorial1
    cobraToGurobiProb getEssentialRxns optimizeProb tutorial2
    cobraToMosekRes getExchangeRxns parseFormulas tutorial2_solutions
    colorPathway getExpressionStructure parseHPA tutorial3
    colorSubsystem getFluxZ parseHPArna tutorial3_solutions
    combineMetaCycKEGGModels getFullPath parseRxnEqu tutorial4
    compareModels getGenesFromKEGG parseScores tutorial4_solutions
    compareMultipleModels getINITModel parseTaskList tutorial5
    constructEquations getIndexes permuteModel tutorial6
    constructMultiFasta getKEGGModelForOrganism plotAdditionalInfo updateDocumentation
    constructPathwayFromCelldesigner getMILPParams plotLabels writeSheet
    constructS getMetaCycModelForOrganism predictLocalization writeYaml
    consumeSomething getMetsFromKEGG printFluxes
    contractModel getMetsFromMetaCyc printModel
    convertToIrrev getMetsInComp printModelStats
    copyToComps getMinNrFluxes qMOMA
    + FSEOF copyToComps getMetsInComp printFluxes + SBMLFromExcel deleteUnusedGenes getMinNrFluxes printModel + addExchangeRxns diamondTests getModelFromHomology printModelStats + addGenesRaven dispEM getModelFromKEGG qMOMA + addJavaPaths drawMap getModelFromMetaCyc randomSampling + addMets drawPathway getObjectiveString ravenCobraWrapper + addRavenToUserPath expandModel getPathwayDimensions removeBadRxns + addRxns exportForGit getPhylDist removeGenes + addRxnsGenesMets exportModel getRxnsFromKEGG removeMets + addSpontaneousRxns exportModelToSIF getRxnsFromMetaCyc removeReactions + addTransport exportToExcelFormat getRxnsInComp replaceMets + analyzeSampling exportToTabDelimited getToolboxVersion reporterMetabolites + blastPlusTests extractMiriam getTransportRxns runINIT + buildEquation fillGaps getWSLpath scoreModel + canConsume findGeneDeletions getWoLFScores setColorToMapRxns + canProduce fitParameters guessComposition setExchangeBounds + cdhitTests fitTasks gurobiToCobraRes setOmicDataToRxns + changeGeneAssoc followChanged haveFlux setParam + changeGrRules followFluxes hmmerTests setRavenSolver + changeRxns gapReport importExcelModel setTitle + checkFileExistence generateNewIds importModel simplifyModel + checkFunctionUniqueness getAllRxnsFromGenes linkMetaCycKEGGRxns solveLP + checkInstallation getAllSubGraphs loadSheet solveQP + checkModelStruct getAllowedBounds loadWorkbook sortIdentifiers + checkProduction getBlast mafftTests sortIdentifiers_and_permuteModelTests + checkRxn getBlastFromExcel makeFakeBlastStructure sortModel + checkSolution getColorCodes makeSomething standardizeGrRules + checkTasks getDiamond mapCompartments standardizeModelFieldOrder + cleanSheet getElementalBalance mapPathwayRxnNames startup + closeModel getEnzymesFromMetaCyc markPathwayWithExpression tinitTests + cobraToGurobiProb getEssentialRxns markPathwayWithFluxes trimPathway + cobraToMosekRes getExchangeRxns mergeCompartments tutorial1 + colorPathway getExpressionStructure mergeModels tutorial2 + colorSubsystem getFluxZ optimizeProb tutorial2_solutions + combineMetaCycKEGGModels getFullPath parseFormulas tutorial3 + compareMultipleModels getGenesFromKEGG parseHPA tutorial3_solutions + compareRxnsGenesMetsComps getINITModel parseHPArna tutorial4 + constructEquations getIndexes parseRxnEqu tutorial4_solutions + constructMultiFasta getKEGGModelForOrganism parseScores tutorial5 + constructPathwayFromCelldesigner getMD5Hash parseTaskList tutorial6 + constructS getMILPParams permuteModel updateDocumentation + consumeSomething getMetaCycModelForOrganism plotAdditionalInfo writeSheet + contractModel getMetsFromKEGG plotLabels writeYaml + convertToIrrev getMetsFromMetaCyc predictLocalization
    Generated by m2html © 2005
    diff --git a/doc/installation/checkFunctionUniqueness.html b/doc/installation/checkFunctionUniqueness.html index 1d804c53..7348b95a 100644 --- a/doc/installation/checkFunctionUniqueness.html +++ b/doc/installation/checkFunctionUniqueness.html @@ -40,7 +40,7 @@

    CROSS-REFERENCE INFORMATION ^ </ul> This function is called by: <ul style= -
  • checkInstallation checkInstallation
    • +
  • checkInstallation checkInstallation
    • diff --git a/doc/installation/checkInstallation.html b/doc/installation/checkInstallation.html index b0381763..a60fd0cd 100644 --- a/doc/installation/checkInstallation.html +++ b/doc/installation/checkInstallation.html @@ -24,7 +24,7 @@

    PURPOSE ^checkInstallation

    SYNOPSIS ^

    -
    function checkInstallation()
    +
    function checkInstallation(develMode)

    DESCRIPTION ^

     checkInstallation
@@ -33,7 +33,12 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -45,204 +50,180 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 <!-- crossreference -->
 
-
+<h2><a name=SUBFUNCTIONS ^
    
+
 
 
    SOURCE CODE ^
    
-
    0001 function checkInstallation()
+
    0001 function checkInstallation(develMode)
 0002 % checkInstallation
 0003 %   The purpose of this function is to check if all necessary functions are
 0004 %   installed and working. It also checks whether there are any functions
 0005 %   with overlapping names between RAVEN and other toolboxes or
 0006 %   user-defined functions, which are accessible from MATLAB pathlist
 0007 %
-0008 %   Usage: checkInstallation()
-0009 
-0010 %Check if RAVEN is in the MATLAB path list
-0011 paths=textscan(path,'%s','delimiter', pathsep);
-0012 paths=paths{1};
-0013 
-0014 %Get the RAVEN path
-0015 [ST, I]=dbstack('-completenames');
-0016 [ravenDir,~,~]=fileparts(fileparts(ST(I).file));
-0017 
-0018 %Print the RAVEN version if it is not the development version
-0019 if exist(fullfile(ravenDir,'version.txt'), 'file') == 2
-0020     fprintf(['\n*** THE RAVEN TOOLBOX v.' fgetl(fopen(fullfile(ravenDir,'version.txt'))) ' ***\n\n']);
-0021 else
-0022     fprintf('\n*** THE RAVEN TOOLBOX - DEVELOPMENT VERSION ***\n\n');
-0023 end
-0024 
-0025 fprintf('Checking if RAVEN is on the MATLAB path...\t\t\t\t\t\t\t\t\t');
-0026 if ismember(ravenDir,paths)
-0027     fprintf('OK\n');
-0028 else
-0029     fprintf('OK (just added)\n');
-0030     subpath=regexp(genpath(ravenDir),pathsep,'split'); %List all subdirectories
-0031     pathsToKeep=cellfun(@(x) isempty(strfind(x,'.git')),subpath) & cellfun(@(x) isempty(strfind(x,'doc')),subpath);
-0032     addpath(strjoin(subpath(pathsToKeep),pathsep));
-0033     savepath
-0034 end
+0008 %   Input:
+0009 %   develMode       logical indicating development mode, which includes
+0010 %                   testing of binaries that are required to update KEGG
+0011 %                   HMMs (opt, default false)
+0012 %
+0013 %   Usage: checkInstallation(develMode)
+0014 
+0015 if nargin<1
+0016     develMode=false;
+0017 end
+0018 
+0019 %Check if RAVEN is in the MATLAB path list
+0020 paths=textscan(path,'%s','delimiter', pathsep);
+0021 paths=paths{1};
+0022 
+0023 %Get the RAVEN path
+0024 [ST, I]=dbstack('-completenames');
+0025 [ravenDir,~,~]=fileparts(fileparts(ST(I).file));
+0026 
+0027 %Print the RAVEN version if it is not the development version
+0028 if exist(fullfile(ravenDir,'version.txt'), 'file') == 2
+0029     fprintf(['\n*** THE RAVEN TOOLBOX v.' fgetl(fopen(fullfile(ravenDir,'version.txt'))) ' ***\n\n']);
+0030 else
+0031     fprintf('\n*** THE RAVEN TOOLBOX - DEVELOPMENT VERSION ***\n\n');
+0032 end
+0033 
+0034 fprintf(['MATLAB R' version('-release') ' detected\n\n']);
 0035 
-0036 %Add the required classes to the static Java path if not already added
-0037 addJavaPaths();
-0038 
-0039 excelFile=fullfile(ravenDir,'tutorial','empty.xlsx');
-0040 xmlFile=fullfile(ravenDir,'tutorial','empty.xml');
-0041 matFile=fullfile(ravenDir,'tutorial','empty.mat');
-0042 
-0043 %Check if it is possible to parse an Excel file
-0044 fprintf('Checking if it is possible to parse a model in Microsoft Excel format...\t');
-0045 try
-0046     importExcelModel(excelFile,false,false,true);
-0047     fprintf('OK\n');
-0048 catch
-0049     fprintf('Not OK\n');
-0050 end
-0051 
-0052 %Check if it is possible to import an SBML model using libSBML
-0053 fprintf('Checking if it is possible to import an SBML model using libSBML...\t\t\t');
-0054 try
-0055     importModel(xmlFile);
-0056     try
-0057         libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+
-0058         fprintf('OK\n');
-0059     catch
-0060         fprintf(['Not OK\n\n'...
-0061             'An older libSBML version was found, update to version 5.17.0 or higher\n'...
-0062             'for a significant improvement of model import\n\n']);
-0063     end
-0064 catch
-0065     fprintf(['Not OK\nTo import SBML models, download libSBML from\n'...
-0066         'http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n']);
-0067 end
-0068 
-0069 %Define values for keepSolver and workingSolvers, needed for solver
-0070 %functionality check
-0071 keepSolver=false;
-0072 workingSolvers='';
-0073 %Get current solver. Set it to 'none', if it is not set
-0074 if ~ispref('RAVEN','solver')
-0075     fprintf('Solver found in preferences... NONE\n');
-0076     setRavenSolver('none');
-0077     curSolv=getpref('RAVEN','solver');
-0078 else
-0079     curSolv=getpref('RAVEN','solver');
-0080     fprintf(['Solver found in preferences... ',curSolv,'\n']);
-0081 end
-0082 
-0083 %Check if it is possible to solve an LP problem using different solvers
-0084 solver={'gurobi','cobra'};
-0085 
-0086 for i=1:numel(solver)
-0087     fprintf(['Checking if it is possible to solve an LP problem using ',solver{i},'...\t\t\t']);
-0088     try
-0089         setRavenSolver(solver{i});
-0090         load(matFile);
-0091         solveLP(emptyModel);
-0092         workingSolvers=strcat(workingSolvers,';',solver{i});
-0093         fprintf('OK\n');
-0094         if strcmp(curSolv,solver{i})
-0095             keepSolver=true;
-0096         end
-0097     catch
-0098         fprintf('Not OK\n');
-0099     end
-0100 end
-0101 
-0102 if keepSolver
-0103     %The solver set in curSolv is functional, so the settings are restored
-0104     %to the ones which were set before running checkInstallation
-0105     setRavenSolver(curSolv);
-0106     fprintf(['Preferred solver... KEPT\nSolver saved as preference... ',curSolv,'\n\n']);
-0107 elseif ~isempty(workingSolvers)
-0108     %There are working solvers, but the none of them is the solver defined
-0109     %by curSolv. The first working solver is therefore set as RAVEN solver
-0110     workingSolvers=regexprep(workingSolvers,'^;','');
-0111     workingSolvers=regexprep(workingSolvers,';.+$','');
-0112     %Only one working solver should be left by now in workingSolvers
-0113     setRavenSolver(workingSolvers);
-0114     fprintf(['Preferred solver... NEW\nSolver saved as preference... ',workingSolvers,'\n\n']);
-0115 else
-0116     %No functional solvers were found, so the setting is restored back to
-0117     %original
-0118     setRavenSolver(curSolv);
-0119     fprintf(['WARNING: No working solver was found!\n'...
-0120         'Install the solver, set it using setRavenSolver(''solverName'') and run checkInstallation again\n'...
-0121         'Available solverName options are ''mosek'', ''gurobi'' and ''cobra''\n\n']);
-0122 end
-0123 
-0124 if ismac
-0125     binEnd='.mac';
-0126 elseif isunix
-0127     binEnd='';
-0128 elseif ispc
-0129     binEnd='.exe';
-0130 end
-0131 fprintf('Checking essential binary executables:\n');
-0132 fprintf('NOTE: Broken binary executables <strong>must be fixed</strong> before running RAVEN\n');
-0133 fprintf(['\tmakeblastdb' binEnd '...\t\t\t\t\t\t\t']);
-0134 [res,~]=system(['"' fullfile(ravenDir,'software','blast+',['makeblastdb' binEnd]) '"']);
-0135 if res==1
-0136     fprintf('OK\n');
-0137 else
-0138     fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-0139 end
-0140 fprintf(['\tblastp' binEnd '...\t\t\t\t\t\t\t\t']);
-0141 [res,~]=system(['"' fullfile(ravenDir,'software','blast+',['blastp' binEnd]) '"']);
-0142 if res==1
-0143     fprintf('OK\n');
-0144 else
-0145     fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-0146 end
-0147 fprintf(['\tdiamond' binEnd '...\t\t\t\t\t\t\t\t']);
-0148 [res,~]=system(['"' fullfile(ravenDir,'software','diamond',['diamond' binEnd]) '"']);
-0149 if res==1
-0150     fprintf('OK\n');
-0151 else
-0152     fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-0153 end
-0154 fprintf(['\thmmsearch' binEnd '...\t\t\t\t\t\t\t']);
-0155 [res,~]=system(['"' fullfile(ravenDir,'software','hmmer',['hmmsearch' binEnd]) '"']);
-0156 if res==1
-0157     fprintf('OK\n');
-0158 else
-0159     fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-0160 end
-0161 fprintf('Checking non-essential/development binary executables:\n');
-0162 fprintf('NOTE: Only fix these binaries if planning to use KEGG FTP dump files in getKEGGModelForOrganism\n');
-0163 fprintf(['\tcd-hit' binEnd '...\t\t\t\t\t\t\t\t']);
-0164 [res,~]=system(['"' fullfile(ravenDir,'software','cd-hit',['cd-hit' binEnd]) '"']);
-0165 if res==1
-0166     fprintf('OK\n');
-0167 else
-0168     fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
-0169 end
-0170 fprintf('\tmafft.bat...\t\t\t\t\t\t\t\t');
-0171 if ismac
-0172     [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-mac','mafft.bat') '" --help ']);
-0173 elseif isunix
-0174     [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-linux64','mafft.bat') '" --help ']);
-0175 elseif ispc
-0176     [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-win','mafft.bat') '" --help ']);
-0177 end
-0178 if res==1
-0179     fprintf('OK\n');
-0180 else
-0181     fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
-0182 end
-0183 fprintf(['\thmmbuild' binEnd '...\t\t\t\t\t\t\t\t']);
-0184 [res,~]=system(['"' fullfile(ravenDir,'software','hmmer',['hmmbuild' binEnd]) '"']);
-0185 if res==1
-0186     fprintf('OK\n\n');
-0187 else
-0188     fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
-0189 end
-0190 
-0191 fprintf('Checking whether RAVEN functions are non-redundant across MATLAB path...\t');
-0192 checkFunctionUniqueness();
-0193 
-0194 fprintf('\n*** checkInstallation complete ***\n\n');
-0195 end
    
+0036 fprintf('Checking if RAVEN is on the MATLAB path...\t\t\t\t\t\t\t\t\t');
+0037 if ismember(ravenDir,paths)
+0038     fprintf('OK\n');
+0039 else
+0040     fprintf('OK (just added)\n');
+0041     subpath=regexp(genpath(ravenDir),pathsep,'split'); %List all subdirectories
+0042     pathsToKeep=cellfun(@(x) isempty(strfind(x,'.git')),subpath) & cellfun(@(x) isempty(strfind(x,'doc')),subpath);
+0043     addpath(strjoin(subpath(pathsToKeep),pathsep));
+0044     savepath
+0045 end
+0046 
+0047 %Add the required classes to the static Java path if not already added
+0048 addJavaPaths();
+0049 
+0050 excelFile=fullfile(ravenDir,'tutorial','empty.xlsx');
+0051 xmlFile=fullfile(ravenDir,'tutorial','empty.xml');
+0052 matFile=fullfile(ravenDir,'tutorial','empty.mat');
+0053 
+0054 %Check if it is possible to parse an Excel file
+0055 fprintf('Checking if it is possible to parse a model in Microsoft Excel format...\t');
+0056 try
+0057     importExcelModel(excelFile,false,false,true);
+0058     fprintf('OK\n');
+0059 catch
+0060     fprintf('Not OK\n');
+0061 end
+0062 
+0063 %Check if it is possible to import an SBML model using libSBML
+0064 fprintf('Checking if it is possible to import an SBML model using libSBML...\t\t\t');
+0065 try
+0066     importModel(xmlFile);
+0067     try
+0068         libSBMLver=OutputSBML; % Only works in libSBML 5.17.0+
+0069         fprintf('OK\n');
+0070     catch
+0071         fprintf(['Not OK\n\n'...
+0072             'An older libSBML version was found, update to version 5.17.0 or higher\n'...
+0073             'for a significant improvement of model import\n\n']);
+0074     end
+0075 catch
+0076     fprintf(['Not OK\nTo import SBML models, download libSBML from\n'...
+0077         'http://sbml.org/Software/libSBML/Downloading_libSBML and add to MATLAB path\n']);
+0078 end
+0079 
+0080 %Define values for keepSolver and workingSolvers, needed for solver
+0081 %functionality check
+0082 keepSolver=false;
+0083 workingSolvers='';
+0084 %Get current solver. Set it to 'none', if it is not set
+0085 if ~ispref('RAVEN','solver')
+0086     fprintf('Solver found in preferences... NONE\n');
+0087     setRavenSolver('none');
+0088     curSolv=getpref('RAVEN','solver');
+0089 else
+0090     curSolv=getpref('RAVEN','solver');
+0091     fprintf(['Solver found in preferences... ',curSolv,'\n']);
+0092 end
+0093 
+0094 %Check if it is possible to solve an LP problem using different solvers
+0095 solver={'gurobi','cobra'};
+0096 
+0097 for i=1:numel(solver)
+0098     fprintf(['Checking if it is possible to solve an LP problem using ',solver{i},'...\t\t\t']);
+0099     try
+0100         setRavenSolver(solver{i});
+0101         load(matFile);
+0102         solveLP(emptyModel);
+0103         workingSolvers=strcat(workingSolvers,';',solver{i});
+0104         fprintf('OK\n');
+0105         if strcmp(curSolv,solver{i})
+0106             keepSolver=true;
+0107         end
+0108     catch
+0109         fprintf('Not OK\n');
+0110     end
+0111 end
+0112 
+0113 if keepSolver
+0114     %The solver set in curSolv is functional, so the settings are restored
+0115     %to the ones which were set before running checkInstallation
+0116     setRavenSolver(curSolv);
+0117     fprintf(['Preferred solver... KEPT\nSolver saved as preference... ',curSolv,'\n\n']);
+0118 elseif ~isempty(workingSolvers)
+0119     %There are working solvers, but the none of them is the solver defined
+0120     %by curSolv. The first working solver is therefore set as RAVEN solver
+0121     workingSolvers=regexprep(workingSolvers,'^;','');
+0122     workingSolvers=regexprep(workingSolvers,';.+$','');
+0123     %Only one working solver should be left by now in workingSolvers
+0124     setRavenSolver(workingSolvers);
+0125     fprintf(['Preferred solver... NEW\nSolver saved as preference... ',workingSolvers,'\n\n']);
+0126 else
+0127     %No functional solvers were found, so the setting is restored back to
+0128     %original
+0129     setRavenSolver(curSolv);
+0130     fprintf(['WARNING: No working solver was found!\n'...
+0131         'Install the solver, set it using setRavenSolver(''solverName'') and run checkInstallation again\n'...
+0132         'Available solverName options are ''gurobi'' and ''cobra''\n\n']);
+0133 end
+0134 
+0135 fprintf('Checking essential binary executables:\n');
+0136 
+0137 fprintf('\tBLAST+... ');
+0138 res=runtests('blastPlusTests.m','OutputDetail',0);
+0139 interpretResults(res);
+0140 fprintf('\tDIAMOND... ');
+0141 res=runtests('diamondTests.m','OutputDetail',0);
+0142 interpretResults(res);
+0143 fprintf('\tHMMER... ');
+0144 res=runtests('hmmerTests.m','OutputDetail',0);
+0145 interpretResults(res);
+0146 
+0147 if develMode
+0148     fprintf('NOTE: Only fix these binaries if planning to use KEGG FTP dump files in getKEGGModelForOrganism\n');
+0149     fprintf('\tCD-HIT... ');
+0150     res=runtests('cdhitTests.m','OutputDetail',0);
+0151     interpretResults(res);
+0152     fprintf('\tMAFFT... ');
+0153     res=runtests('mafftTests.m','OutputDetail',0);
+0154     interpretResults(res);
+0155 end
+0156 
+0157 fprintf('Checking whether RAVEN functions are non-redundant across MATLAB path...\t');
+0158 checkFunctionUniqueness();
+0159 
+0160 fprintf('\n*** checkInstallation complete ***\n\n');
+0161 end
+0162 
+0163 function interpretResults(results)
+0164 if results.Failed==0 && results.Incomplete==0
+0165     fprintf('OK\n');
+0166 else
+0167     fprintf('Not OK! Download/compile the binary and rerun checkInstallation\n');
+0168 end
+0169 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/SBMLFromExcel.html b/doc/io/SBMLFromExcel.html
index 9799b702..34b74dae 100644
--- a/doc/io/SBMLFromExcel.html
+++ b/doc/io/SBMLFromExcel.html
@@ -49,7 +49,7 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • exportModel	exportModel
  • importExcelModel	importExcelModel
    • 
 This function is called by:
 
@@ -86,7 +86,7 @@ 
    SOURCE CODE ^importExcelModel(fileName,false,printWarnings);
 0028 printModelStats(model,printWarnings,false);
-0029 exportModel(model,outputFileName,toCOBRA,true);
+0029 exportModel(model,outputFileName,toCOBRA,true);
 0030 end
    Generated by m2html © 2005
    diff --git a/doc/io/checkFileExistence.html b/doc/io/checkFileExistence.html index 703f1c0d..7e61f5d9 100644 --- a/doc/io/checkFileExistence.html +++ b/doc/io/checkFileExistence.html @@ -24,7 +24,7 @@

    PURPOSE ^checkFileExistence

    SYNOPSIS ^

    -
    function files=checkFileExistence(files,makeFullPath,allowSpace)
    +
    function files=checkFileExistence(files,fullOrTemp,allowSpace)

    DESCRIPTION ^

     checkFileExistence
@@ -35,13 +35,20 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -50,13 +57,13 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
+
  • getMD5Hash	getMD5Hash
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function files=checkFileExistence(files,makeFullPath,allowSpace)
+
    0001 function files=checkFileExistence(files,fullOrTemp,allowSpace)
 0002 % checkFileExistence
 0003 %   Check whether files exist. If no full path is given a file should be
 0004 %   located in the current folder, which by default is appended to the
@@ -65,46 +72,69 @@ 
    SOURCE CODE ^%   Input:
 0008 %   files           string or cell array of strings with path to file(s) or
 0009 %                   path or filename(s)
-0010 %   makeFullPath    logical, whether files located in the current folder
-0011 %                   should be provided with the full path (opt, default
-0012 %                   true)
-0013 %   allowSpace      logical, whether 'space' character is allowed in the
-0014 %                   path (opt, default true)
-0015 %
-0016 %   Usage: files=checkFileExistence(files,makeFullPath,allowSpace)
-0017 
-0018 if nargin<2
-0019     makeFullPath = true;
-0020 end
-0021 if nargin<3
-0022     allowSpace = true;
-0023 end
+0010 %   fullOrTemp      0: do not change path to file(s)
+0011 %                   1: return full path to file(s)
+0012 %                   2: copy file(s) to system default temporary folder and
+0013 %                      return full path
+0014 %                   (opt, default 0)
+0015 %   allowSpace      logical, whether 'space' character is allowed in the
+0016 %                   path (opt, default true)
+0017 %
+0018 %   Output:
+0019 %   files           string or cell array of strings with updated paths if
+0020 %                   fullOrTemp was set as 1 or 2, otherwise original paths
+0021 %                   are returned
+0022 %
+0023 %   Usage: files=checkFileExistence(files,fullOrTemp,allowSpace)
 0024 
-0025 if isstr(files)
-0026     oneFile=true;
-0027     files={files};
-0028 else
-0029     oneFile=false;
+0025 if nargin<2
+0026     fullOrTemp = 0;
+0027 end
+0028 if nargin<3
+0029     allowSpace = true;
 0030 end
-0031 filesOriginal = files;
-0032 
-0033 inCurrDir = ~contains(files,'\') & ~contains(files,'/');
-0034 files(inCurrDir) = fullfile(cd,files(inCurrDir));
-0035 
-0036 for i=1:numel(files)
-0037     if ~exist(files{i},'file')
-0038         error('File "%s" cannot be found\n',files{i});
-0039     elseif allowSpace == true & strfind(files{i},' ')
-0040         error('File "%s" has an invalid space in the filename or path, please remove this before running this function\n',files{i});
-0041     end
-0042 end
-0043 
-0044 if makeFullPath == false
-0045     files = filesOriginal;
-0046 end
-0047 if oneFile == true
-0048     files = files{1};
-0049 end
    
+0031 
+0032 if isstr(files)
+0033     oneFile=true;
+0034     files={files};
+0035 else
+0036     oneFile=false;
+0037 end
+0038 filesOriginal = files;
+0039 
+0040 %Make all full paths before check of file existence
+0041 if ispc % full path starts like "C:\"
+0042     inCurrDir = cellfun(@isempty,regexpi(files,'^[a-z]\:\\'));
+0043 else %isunix full path starts like "/"
+0044     inCurrDir = cellfun(@isempty,regexpi(files,'\/'));
+0045 end
+0046 files(inCurrDir) = fullfile(cd,files(inCurrDir));
+0047 
+0048 %Check existence
+0049 for i=1:numel(files)
+0050     if ~exist(files{i},'file')
+0051         error('File "%s" cannot be found\n',files{i});
+0052     elseif allowSpace == false & strfind(files{i},' ')
+0053         error('File "%s" has an invalid space in the filename or path, please remove this before running this function\n',files{i});
+0054     end
+0055 end
+0056 
+0057 switch fullOrTemp
+0058     case 0
+0059         files = filesOriginal;
+0060     case 1
+0061         % files already contains full path
+0062     case 2
+0063         for i=1:numel(files)
+0064             tmpFile=tempname;
+0065             copyfile(files{i},tmpFile);
+0066             files{i}=tmpFile;
+0067         end
+0068 end
+0069 
+0070 if oneFile == true
+0071     files = files{1};
+0072 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportForGit.html b/doc/io/exportForGit.html
index 82d9dc3b..43f5ef74 100644
--- a/doc/io/exportForGit.html
+++ b/doc/io/exportForGit.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportForGit

    SYNOPSIS ^

    -
    function out=exportForGit(model,prefix,path,formats,masterFlag,subDirs)
    +
    function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs)

    DESCRIPTION ^

     exportForGit
@@ -41,8 +41,8 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • exportModel	exportModel
  • exportToExcelFormat	exportToExcelFormat
  • getToolboxVersion	getToolboxVersion
  • sortIdentifiers	exportModel
  • writeYaml	writeYaml
    • 
 This function is called by:
 
@@ -65,7 +65,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 
 
 <h2><a name=SOURCE CODE ^
    
-
    0001 function out=exportForGit(model,prefix,path,formats,masterFlag,subDirs)
+
    0001 function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs)
 0002 % exportForGit
 0003 %   Generates a directory structure and populates this with model files, ready
 0004 %   to be commited to a Git(Hub) maintained model repository. Writes the model
@@ -80,8 +80,8 @@ 
    SOURCE CODE ^%   formats             cell array of strings specifying in what file formats
 0014 %                       the model should be exported (opt, default to all
 0015 %                       formats as {'mat', 'txt', 'xlsx', 'xml', 'yml'})
-0016 %   masterFlag          logical, if true, function will error if RAVEN (and
-0017 %                       COBRA if detected) is/are not on the master branch.
+0016 %   mainBranchFlag          logical, if true, function will error if RAVEN (and
+0017 %                       COBRA if detected) is/are not on the main branch.
 0018 %                       (opt, default false)
 0019 %   subDirs             logical, whether model files for each file format
 0020 %                       should be written in its own subdirectory, with
@@ -89,12 +89,12 @@ 
    SOURCE CODE ^%                       standard-GEM repository format. If false, all files
 0023 %                       are stored in the same folder. (opt, default true)
 0024 %
-0025 %   Usage: exportForGit(model,prefix,path,formats,masterFlag)
+0025 %   Usage: exportForGit(model,prefix,path,formats,mainBranchFlag)
 0026 if nargin<6
 0027     subDirs=true;
 0028 end
 0029 if nargin<5
-0030     masterFlag=false;
+0030     mainBranchFlag=false;
 0031 end
 0032 if nargin<4 || isempty(formats)
 0033     formats={'mat', 'txt', 'xlsx', 'xml', 'yml'};
@@ -113,91 +113,94 @@ 
    SOURCE CODE ^'model';
 0047 end
 0048 
-0049 %Get versions or commits of toolboxes:
-0050 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',masterFlag);
-0051 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',masterFlag);
-0052 
-0053 %Retrieve libSBML version:
-0054 try % 5.17.0 and newer
-0055     libSBMLver=OutputSBML;
-0056     libSBMLver=libSBMLver.libSBML_version_string;
-0057 catch % before 5.17.0
-0058     fid = fopen('tempModelForLibSBMLversion.xml','w+');
-0059     fclose(fid);
-0060     evalc('[~,~,libSBMLver]=TranslateSBML(''tempModelForLibSBMLversion.xml'',0,0)');
-0061     libSBMLver=libSBMLver.libSBML_version_string;
-0062     delete('tempModelForLibSBMLversion.xml');
-0063 end
-0064 
-0065 % Make models folder, no warnings if folder already exists
-0066 if subDirs
-0067     path=fullfile(path,'model');
-0068     filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'});
-0069     [~,~,~]=mkdir(path);
-0070     for i = 1:length(formats)
-0071         [~,~,~]=mkdir(fullfile(path,formats{i}));
-0072     end
-0073 else
-0074     filePath=cell(1,5); filePath(:)={path};
-0075 end
-0076 
-0077 
-0078 % Write TXT format
-0079 if ismember('txt', formats)
-0080     fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w');
-0081     eqns=constructEquations(model,model.rxns,false,false,false,true);
-0082     eqns=strrep(eqns,' => ','  -> ');
-0083     eqns=strrep(eqns,' <=> ','  <=> ');
-0084     eqns=regexprep(eqns,'> $','>');
-0085     grRules=regexprep(model.grRules,'\((?!\()','( ');
-0086     grRules=regexprep(grRules,'(?<!\))\)',' )');
-0087     fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n');
-0088     for i = 1:numel(model.rxns)
-0089         fprintf(fid, '%s\t', model.rxns{i});
-0090         fprintf(fid, '%s \t', eqns{i});
-0091         fprintf(fid, '%s\t', grRules{i});
-0092         fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i));
-0093     end
-0094     fclose(fid);
-0095 end
-0096 
-0097 % Write YML format
-0098 if ismember('yml', formats)
-0099     writeYaml(model,fullfile(filePath{2},strcat(prefix,'.yml')));
-0100 end
-0101 
-0102 % Write MAT format
-0103 if ismember('mat', formats)
-0104     save(fullfile(filePath{3},strcat(prefix,'.mat')),'model');
-0105 end
-0106 
-0107 % Write XLSX format
-0108 if ismember('xlsx', formats)
-0109     exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx')));
-0110 end
-0111 
-0112 % Write XML format
-0113 if ismember('xml', formats)
-0114         exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')));
-0115 end
-0116 
-0117 %Save file with versions:
-0118 fid = fopen(fullfile(path,'dependencies.txt'),'wt');
-0119 fprintf(fid,['MATLAB\t' version '\n']);
-0120 fprintf(fid,['libSBML\t' libSBMLver '\n']);
-0121 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']);
-0122 if ~isempty(COBRAver)
-0123     fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']);
-0124 end
-0125 if isfield(model,'modelVersion')
-0126     fields = fieldnames(model.modelVersion);
-0127     for i = 1:length(fields)
-0128         value = model.modelVersion.(fields{i});
-0129         fprintf(fid,[fields{i} '\t' num2str(value) '\n']);
-0130     end
-0131 end
-0132 fclose(fid);
-0133 end
    
+0049 %Sort reactions, metabolites and genes alphabetically
+0050 model=sortIdentifiers(model);
+0051 
+0052 %Get versions or commits of toolboxes:
+0053 RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
+0054 COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
+0055 
+0056 %Retrieve libSBML version:
+0057 try % 5.17.0 and newer
+0058     libSBMLver=OutputSBML;
+0059     libSBMLver=libSBMLver.libSBML_version_string;
+0060 catch % before 5.17.0
+0061     fid = fopen('tempModelForLibSBMLversion.xml','w+');
+0062     fclose(fid);
+0063     evalc('[~,~,libSBMLver]=TranslateSBML(''tempModelForLibSBMLversion.xml'',0,0)');
+0064     libSBMLver=libSBMLver.libSBML_version_string;
+0065     delete('tempModelForLibSBMLversion.xml');
+0066 end
+0067 
+0068 % Make models folder, no warnings if folder already exists
+0069 if subDirs
+0070     path=fullfile(path,'model');
+0071     filePath=strcat(path,filesep,{'txt','yml','mat','xlsx','xml'});
+0072     [~,~,~]=mkdir(path);
+0073     for i = 1:length(formats)
+0074         [~,~,~]=mkdir(fullfile(path,formats{i}));
+0075     end
+0076 else
+0077     filePath=cell(1,5); filePath(:)={path};
+0078 end
+0079 
+0080 
+0081 % Write TXT format
+0082 if ismember('txt', formats)
+0083     fid=fopen(fullfile(filePath{1},strcat(prefix,'.txt')),'w');
+0084     eqns=constructEquations(model,model.rxns,false,false,false,true);
+0085     eqns=strrep(eqns,' => ','  -> ');
+0086     eqns=strrep(eqns,' <=> ','  <=> ');
+0087     eqns=regexprep(eqns,'> $','>');
+0088     grRules=regexprep(model.grRules,'\((?!\()','( ');
+0089     grRules=regexprep(grRules,'(?<!\))\)',' )');
+0090     fprintf(fid, 'Rxn name\tFormula\tGene-reaction association\tLB\tUB\tObjective\n');
+0091     for i = 1:numel(model.rxns)
+0092         fprintf(fid, '%s\t', model.rxns{i});
+0093         fprintf(fid, '%s \t', eqns{i});
+0094         fprintf(fid, '%s\t', grRules{i});
+0095         fprintf(fid, '%6.2f\t%6.2f\t%6.2f\n', model.lb(i), model.ub(i), model.c(i));
+0096     end
+0097     fclose(fid);
+0098 end
+0099 
+0100 % Write YML format
+0101 if ismember('yml', formats)
+0102     writeYaml(model,fullfile(filePath{2},strcat(prefix,'.yml')));
+0103 end
+0104 
+0105 % Write MAT format
+0106 if ismember('mat', formats)
+0107     save(fullfile(filePath{3},strcat(prefix,'.mat')),'model');
+0108 end
+0109 
+0110 % Write XLSX format
+0111 if ismember('xlsx', formats)
+0112     exportToExcelFormat(model,fullfile(filePath{4},strcat(prefix,'.xlsx')));
+0113 end
+0114 
+0115 % Write XML format
+0116 if ismember('xml', formats)
+0117         exportModel(model,fullfile(filePath{5},strcat(prefix,'.xml')));
+0118 end
+0119 
+0120 %Save file with versions:
+0121 fid = fopen(fullfile(path,'dependencies.txt'),'wt');
+0122 fprintf(fid,['MATLAB\t' version '\n']);
+0123 fprintf(fid,['libSBML\t' libSBMLver '\n']);
+0124 fprintf(fid,['RAVEN_toolbox\t' RAVENver '\n']);
+0125 if ~isempty(COBRAver)
+0126     fprintf(fid,['COBRA_toolbox\t' COBRAver '\n']);
+0127 end
+0128 if isfield(model,'modelVersion')
+0129     fields = fieldnames(model.modelVersion);
+0130     for i = 1:length(fields)
+0131         value = model.modelVersion.(fields{i});
+0132         fprintf(fid,[fields{i} '\t' num2str(value) '\n']);
+0133     end
+0134 end
+0135 fclose(fid);
+0136 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportModel.html b/doc/io/exportModel.html
index 336c5367..2f9283c0 100644
--- a/doc/io/exportModel.html
+++ b/doc/io/exportModel.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportModel

    SYNOPSIS ^

    -
    function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
    +
    function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)

    DESCRIPTION ^

     exportModel
@@ -38,18 +38,20 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • SBMLFromExcel	SBMLFromExcel
  • exportForGit	exportForGit
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -57,7 +59,7 @@ 
    SUBFUNCTIONS ^function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
  • function miriamString=getMiriam(miriamStruct)
  • function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
  • function vecT = columnVector(vec)
    • 
 
 
    SOURCE CODE ^
    
-
    0001 function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
+
    0001 function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
 0002 % exportModel
 0003 %   Exports a constraint-based model to an SBML file (L3V1 FBCv2)
 0004 %
@@ -69,795 +71,803 @@ 
    SOURCE CODE ^%                       (opt, default false)
 0011 %   supressWarnings     true if warnings should be supressed (opt, default
 0012 %                       false)
-0013 %
-0014 %
-0015 %   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings)
-0016 if nargin<3
-0017     exportGeneComplexes=false;
-0018 end
-0019 if nargin<4
-0020     supressWarnings=false;
-0021 end
-0022 
-0023 %If no subSystems are defined, then no need to use groups package
-0024 if isfield(model,'subSystems')
-0025     modelHasSubsystems=true;
-0026 else
-0027     modelHasSubsystems=false;
-0028 end
-0029 
-0030 %The default SBML format settings, which are used as input for appropriate
-0031 %libSBML functions to generate the blank SBML model structure before using
-0032 %exporting in with OutputSBML to xml file
-0033 sbmlLevel=3;
-0034 sbmlVersion=1;
-0035 sbmlPackages={'fbc'};
-0036 sbmlPackageVersions=2;
-0037 if modelHasSubsystems
-0038     sbmlPackages={sbmlPackages,'groups'};
-0039     sbmlPackageVersions=[sbmlPackageVersions,1];
-0040 end
-0041 
-0042 %Check if the "unconstrained" field is still present. This shows if
-0043 %exchange metabolites have been removed
-0044 if ~isfield(model,'unconstrained')
-0045     if supressWarnings==false
-0046         EM='There is no unconstrained field in the model structure. This means that no metabolites are considered exchange metabolites';
-0047         dispEM(EM,false);
-0048     end
-0049     model.unconstrained=zeros(numel(model.mets),1);
-0050 end
-0051 
-0052 %If model id and name do not exist, make sure that default
-0053 %strings are included
-0054 if ~isfield(model,'id')
-0055     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
-0056     model.id='blankID';
-0057 end
-0058 if ~isfield(model,'name')
-0059     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
-0060     model.name='blankName';
-0061 end
-0062 
-0063 %Check the model structure
-0064 if supressWarnings==false
-0065     checkModelStruct(model,false);
-0066 end
-0067 
-0068 %Add several blank fields, if they do not exist already. This is to reduce
-0069 %the number of conditions below
-0070 if ~isfield(model,'compMiriams')
-0071     model.compMiriams=cell(numel(model.comps),1);
-0072 end
-0073 if ~isfield(model,'inchis')
-0074     model.inchis=cell(numel(model.mets),1);
-0075 end
-0076 if ~isfield(model,'metFormulas')
-0077     model.metFormulas=cell(numel(model.mets),1);
-0078 end
-0079 if ~isfield(model,'metMiriams')
-0080     model.metMiriams=cell(numel(model.mets),1);
-0081 end
-0082 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
-0083     model.geneMiriams=cell(numel(model.genes),1);
-0084 end
-0085 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
-0086     model.geneShortNames=cell(numel(model.genes),1);
-0087 end
-0088 if ~isfield(model,'subSystems')
-0089     model.subSystems=cell(numel(model.rxns),1);
-0090 end
-0091 if ~isfield(model,'eccodes')
-0092     model.eccodes=cell(numel(model.rxns),1);
-0093 end
-0094 if ~isfield(model,'rxnReferences')
-0095     model.rxnReferences=cell(numel(model.rxns),1);
-0096 end
-0097 if ~isfield(model,'rxnConfidenceScores')
-0098     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
-0099 end
-0100 if ~isfield(model,'rxnNotes')
-0101     model.rxnNotes=cell(numel(model.rxns),1);
-0102 end
-0103 if ~isfield(model,'rxnMiriams')
-0104     model.rxnMiriams=cell(numel(model.rxns),1);
-0105 end
-0106 
-0107 if sbmlLevel<3
-0108     %Check if genes have associated compartments
-0109     if ~isfield(model,'geneComps') && isfield(model,'genes')
-0110         if supressWarnings==false
-0111             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
-0112             dispEM(EM,false);
-0113         end
-0114         model.geneComps=ones(numel(model.genes),1);
-0115     end
-0116 end
-0117 
-0118 %Convert ids to SBML-convenient format. This is to avoid the data loss when
-0119 %unsupported characters are included in ids. Here we are using part from
-0120 %convertSBMLID, originating from the COBRA Toolbox
-0121 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0122 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0123 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0124 if isfield(model,'genes')
-0125     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
-0126     originalGenes=model.genes(problemGenes);
-0127     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
-0128     model.genes(problemGenes)=replacedGenes;
-0129     for i=1:numel(problemGenes)
-0130         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
-0131     end
-0132 end
-0133 
-0134 %Generate an empty SBML structure
-0135 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0136 modelSBML.metaid=model.id;
-0137 modelSBML.id=model.id;
-0138 modelSBML.name=model.name;
-0139 
-0140 if isfield(model,'annotation')
-0141     if isfield(model.annotation,'note')
-0142         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
-0143     end
-0144 else
-0145     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
-0146 end
+0013 %   sortIds             logical whether metabolites, reactions and genes
+0014 %                       should be sorted alphabetically by their
+0015 %                       identifiers (opt, default false)
+0016 %
+0017 %   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
+0018 if nargin<3
+0019     exportGeneComplexes=false;
+0020 end
+0021 if nargin<4
+0022     supressWarnings=false;
+0023 end
+0024 if nargin<5
+0025     sortIds=false;
+0026 end
+0027 if sortIds==true
+0028     model=sortIdentifiers(model);
+0029 end
+0030 
+0031 %If no subSystems are defined, then no need to use groups package
+0032 if isfield(model,'subSystems')
+0033     modelHasSubsystems=true;
+0034 else
+0035     modelHasSubsystems=false;
+0036 end
+0037 
+0038 %The default SBML format settings, which are used as input for appropriate
+0039 %libSBML functions to generate the blank SBML model structure before using
+0040 %exporting in with OutputSBML to xml file
+0041 sbmlLevel=3;
+0042 sbmlVersion=1;
+0043 sbmlPackages={'fbc'};
+0044 sbmlPackageVersions=2;
+0045 if modelHasSubsystems
+0046     sbmlPackages={sbmlPackages,'groups'};
+0047     sbmlPackageVersions=[sbmlPackageVersions,1];
+0048 end
+0049 
+0050 %Check if the "unconstrained" field is still present. This shows if
+0051 %exchange metabolites have been removed
+0052 if ~isfield(model,'unconstrained')
+0053     if supressWarnings==false
+0054         EM='There is no unconstrained field in the model structure. This means that no metabolites are considered exchange metabolites';
+0055         dispEM(EM,false);
+0056     end
+0057     model.unconstrained=zeros(numel(model.mets),1);
+0058 end
+0059 
+0060 %If model id and name do not exist, make sure that default
+0061 %strings are included
+0062 if ~isfield(model,'id')
+0063     fprintf('WARNING: The model is missing the "id" field. Uses "blankID". \n');
+0064     model.id='blankID';
+0065 end
+0066 if ~isfield(model,'name')
+0067     fprintf('WARNING: The model is missing the "name" field. Uses "blankName". \n');
+0068     model.name='blankName';
+0069 end
+0070 
+0071 %Check the model structure
+0072 if supressWarnings==false
+0073     checkModelStruct(model,false);
+0074 end
+0075 
+0076 %Add several blank fields, if they do not exist already. This is to reduce
+0077 %the number of conditions below
+0078 if ~isfield(model,'compMiriams')
+0079     model.compMiriams=cell(numel(model.comps),1);
+0080 end
+0081 if ~isfield(model,'inchis')
+0082     model.inchis=cell(numel(model.mets),1);
+0083 end
+0084 if ~isfield(model,'metFormulas')
+0085     model.metFormulas=cell(numel(model.mets),1);
+0086 end
+0087 if ~isfield(model,'metMiriams')
+0088     model.metMiriams=cell(numel(model.mets),1);
+0089 end
+0090 if ~isfield(model,'geneMiriams') && isfield(model,'genes')
+0091     model.geneMiriams=cell(numel(model.genes),1);
+0092 end
+0093 if ~isfield(model,'geneShortNames') && isfield(model,'genes')
+0094     model.geneShortNames=cell(numel(model.genes),1);
+0095 end
+0096 if ~isfield(model,'subSystems')
+0097     model.subSystems=cell(numel(model.rxns),1);
+0098 end
+0099 if ~isfield(model,'eccodes')
+0100     model.eccodes=cell(numel(model.rxns),1);
+0101 end
+0102 if ~isfield(model,'rxnReferences')
+0103     model.rxnReferences=cell(numel(model.rxns),1);
+0104 end
+0105 if ~isfield(model,'rxnConfidenceScores')
+0106     model.rxnConfidenceScores=NaN(numel(model.rxns),1);
+0107 end
+0108 if ~isfield(model,'rxnNotes')
+0109     model.rxnNotes=cell(numel(model.rxns),1);
+0110 end
+0111 if ~isfield(model,'rxnMiriams')
+0112     model.rxnMiriams=cell(numel(model.rxns),1);
+0113 end
+0114 
+0115 if sbmlLevel<3
+0116     %Check if genes have associated compartments
+0117     if ~isfield(model,'geneComps') && isfield(model,'genes')
+0118         if supressWarnings==false
+0119             EM='There are no compartments specified for genes. All genes will be assigned to the first compartment. This is because the SBML structure requires all elements to be assigned to a compartment';
+0120             dispEM(EM,false);
+0121         end
+0122         model.geneComps=ones(numel(model.genes),1);
+0123     end
+0124 end
+0125 
+0126 %Convert ids to SBML-convenient format. This is to avoid the data loss when
+0127 %unsupported characters are included in ids. Here we are using part from
+0128 %convertSBMLID, originating from the COBRA Toolbox
+0129 model.rxns=regexprep(model.rxns,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0130 model.mets=regexprep(model.mets,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0131 model.comps=regexprep(model.comps,'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0132 if isfield(model,'genes')
+0133     problemGenes=find(~cellfun('isempty',regexp(model.genes,'([^0-9_a-zA-Z])')));
+0134     originalGenes=model.genes(problemGenes);
+0135     replacedGenes=regexprep(model.genes(problemGenes),'([^0-9_a-zA-Z])','__${num2str($1+0)}__');
+0136     model.genes(problemGenes)=replacedGenes;
+0137     for i=1:numel(problemGenes)
+0138         model.grRules = regexprep(model.grRules, ['(^|\s|\()' originalGenes{i} '($|\s|\))'], ['$1' replacedGenes{i} '$2']);
+0139     end
+0140 end
+0141 
+0142 %Generate an empty SBML structure
+0143 modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0144 modelSBML.metaid=model.id;
+0145 modelSBML.id=model.id;
+0146 modelSBML.name=model.name;
 0147 
-0148 modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
-0149 if isfield(model,'annotation')
-0150     nameString='';
-0151     if isfield(model.annotation,'familyName')
-0152         if ~isempty(model.annotation.familyName)
-0153             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
-0154         end
-0155     end
-0156     if isfield(model.annotation,'givenName')
-0157         if ~isempty(model.annotation.givenName)
-0158             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
-0159         end
-0160     end
-0161     email='';
-0162     if isfield(model.annotation,'email')
-0163         if ~isempty(model.annotation.email)
-0164             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
-0165         end
-0166     end
-0167     org='';
-0168     if isfield(model.annotation,'organization')
-0169         if ~isempty(model.annotation.organization)
-0170             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
-0171         end
-0172     end
-0173     if ~isempty(nameString) || ~isempty(email) || ~isempty(org)
-0174         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
-0175         if ~isempty(nameString)
-0176             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
-0177         end
-0178         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
-0179     end
-0180 end
-0181 modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
-0182     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
-0183     '</dcterms:created>'...
-0184     '<dcterms:modified rdf:parseType="Resource">'...
-0185     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
-0186     '</dcterms:modified>'];
-0187 
-0188 if isfield(model,'annotation')
-0189     if isfield(model.annotation,'taxonomy')
-0190         modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
-0191     end
-0192 end
-0193 modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
-0194 
-0195 %Prepare compartments
-0196 for i=1:numel(model.comps)
-0197     %Add the default values, as these will be the same in all entries
-0198     if i==1
-0199         if isfield(modelSBML.compartment, 'sboTerm')
-0200             modelSBML.compartment(i).sboTerm=290;
-0201         end
-0202         if isfield(modelSBML.compartment, 'spatialDimensions')
-0203             modelSBML.compartment(i).spatialDimensions=3;
-0204         end
-0205         if isfield(modelSBML.compartment, 'size')
-0206             modelSBML.compartment(i).size=1;
-0207         end
-0208         if isfield(modelSBML.compartment, 'constant')
-0209             modelSBML.compartment(i).constant=1;
-0210         end
-0211         if isfield(modelSBML.compartment, 'isSetSize')
-0212             modelSBML.compartment(i).isSetSize=1;
-0213         end
-0214         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
-0215             modelSBML.compartment(i).isSetSpatialDimensions=1;
-0216         end
-0217     end
-0218     %Copy the default values to the next entry as long as it is not the
-0219     %last one
-0220     if i<numel(model.comps)
-0221         modelSBML.compartment(i+1)=modelSBML.compartment(i);
-0222     end
-0223     
-0224     if isfield(modelSBML.compartment,'metaid')
-0225         if ~isnan(str2double(model.comps(i)))
-0226             EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
-0227             dispEM(EM,false);
-0228             model.comps(i)=strcat('c_',model.comps(i));
-0229         end
-0230         modelSBML.compartment(i).metaid=model.comps{i};
-0231     end
-0232     %Prepare Miriam strings
-0233     if ~isempty(model.compMiriams{i})
-0234         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
-0235         if sbo_ind > 0
-0236             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0237             % remove the SBO term from compMiriams so the information is
-0238             % not duplicated in the "annotation" field later on
-0239             model.compMiriams{i}.name(sbo_ind) = [];
-0240             model.compMiriams{i}.value(sbo_ind) = [];
-0241         end
-0242     end
-0243     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
-0244         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
-0245         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
-0246         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0247     end
-0248     if isfield(modelSBML.compartment, 'name')
-0249         modelSBML.compartment(i).name=model.compNames{i};
+0148 if isfield(model,'annotation')
+0149     if isfield(model.annotation,'note')
+0150         modelSBML.notes=['<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>',regexprep(model.annotation.note,'<p>|</p>',''),'</p></body></notes>'];
+0151     end
+0152 else
+0153     modelSBML.notes='<notes><body xmlns="http://www.w3.org/1999/xhtml"><p>This file was generated using the exportModel function in RAVEN Toolbox 2 and OutputSBML in libSBML </p></body></notes>';
+0154 end
+0155 
+0156 modelSBML.annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.id '">'];
+0157 if isfield(model,'annotation')
+0158     nameString='';
+0159     if isfield(model.annotation,'familyName')
+0160         if ~isempty(model.annotation.familyName)
+0161             nameString=['<vCard:Family>' model.annotation.familyName '</vCard:Family>'];
+0162         end
+0163     end
+0164     if isfield(model.annotation,'givenName')
+0165         if ~isempty(model.annotation.givenName)
+0166             nameString=[nameString '<vCard:Given>' model.annotation.givenName '</vCard:Given>'];
+0167         end
+0168     end
+0169     email='';
+0170     if isfield(model.annotation,'email')
+0171         if ~isempty(model.annotation.email)
+0172             email=['<vCard:EMAIL>' model.annotation.email '</vCard:EMAIL>'];
+0173         end
+0174     end
+0175     org='';
+0176     if isfield(model.annotation,'organization')
+0177         if ~isempty(model.annotation.organization)
+0178             org=['<vCard:ORG rdf:parseType="Resource"><vCard:Orgname>' model.annotation.organization '</vCard:Orgname></vCard:ORG>'];
+0179         end
+0180     end
+0181     if ~isempty(nameString) || ~isempty(email) || ~isempty(org)
+0182         modelSBML.annotation=[modelSBML.annotation '<dc:creator><rdf:Bag><rdf:li rdf:parseType="Resource">'];
+0183         if ~isempty(nameString)
+0184             modelSBML.annotation=[modelSBML.annotation '<vCard:N rdf:parseType="Resource">' nameString '</vCard:N>'];
+0185         end
+0186         modelSBML.annotation=[modelSBML.annotation email org '</rdf:li></rdf:Bag></dc:creator>'];
+0187     end
+0188 end
+0189 modelSBML.annotation=[modelSBML.annotation '<dcterms:created rdf:parseType="Resource">'...
+0190     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
+0191     '</dcterms:created>'...
+0192     '<dcterms:modified rdf:parseType="Resource">'...
+0193     '<dcterms:W3CDTF>' datestr(now,'yyyy-mm-ddTHH:MM:SSZ') '</dcterms:W3CDTF>'...
+0194     '</dcterms:modified>'];
+0195 
+0196 if isfield(model,'annotation')
+0197     if isfield(model.annotation,'taxonomy')
+0198         modelSBML.annotation=[modelSBML.annotation '<bqbiol:is><rdf:Bag><rdf:li rdf:resource="https://identifiers.org/taxonomy/' regexprep(model.annotation.taxonomy,'taxonomy/','') '"/></rdf:Bag></bqbiol:is>'];
+0199     end
+0200 end
+0201 modelSBML.annotation=[modelSBML.annotation '</rdf:Description></rdf:RDF></annotation>'];
+0202 
+0203 %Prepare compartments
+0204 for i=1:numel(model.comps)
+0205     %Add the default values, as these will be the same in all entries
+0206     if i==1
+0207         if isfield(modelSBML.compartment, 'sboTerm')
+0208             modelSBML.compartment(i).sboTerm=290;
+0209         end
+0210         if isfield(modelSBML.compartment, 'spatialDimensions')
+0211             modelSBML.compartment(i).spatialDimensions=3;
+0212         end
+0213         if isfield(modelSBML.compartment, 'size')
+0214             modelSBML.compartment(i).size=1;
+0215         end
+0216         if isfield(modelSBML.compartment, 'constant')
+0217             modelSBML.compartment(i).constant=1;
+0218         end
+0219         if isfield(modelSBML.compartment, 'isSetSize')
+0220             modelSBML.compartment(i).isSetSize=1;
+0221         end
+0222         if isfield(modelSBML.compartment, 'isSetSpatialDimensions')
+0223             modelSBML.compartment(i).isSetSpatialDimensions=1;
+0224         end
+0225     end
+0226     %Copy the default values to the next entry as long as it is not the
+0227     %last one
+0228     if i<numel(model.comps)
+0229         modelSBML.compartment(i+1)=modelSBML.compartment(i);
+0230     end
+0231     
+0232     if isfield(modelSBML.compartment,'metaid')
+0233         if regexp(model.comps{i},'^[^a-zA-Z_]')
+0234             EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
+0235             dispEM(EM,false);
+0236             model.comps(i)=strcat('c_',model.comps(i));
+0237         end
+0238         modelSBML.compartment(i).metaid=model.comps{i};
+0239     end
+0240     %Prepare Miriam strings
+0241     if ~isempty(model.compMiriams{i})
+0242         [~,sbo_ind] = ismember('sbo',model.compMiriams{i}.name);
+0243         if sbo_ind > 0
+0244             modelSBML.compartment(i).sboTerm=str2double(regexprep(model.compMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0245             % remove the SBO term from compMiriams so the information is
+0246             % not duplicated in the "annotation" field later on
+0247             model.compMiriams{i}.name(sbo_ind) = [];
+0248             model.compMiriams{i}.value(sbo_ind) = [];
+0249         end
 0250     end
-0251     if isfield(modelSBML.compartment, 'id')
-0252         modelSBML.compartment(i).id=model.comps{i};
-0253     end
-0254     
-0255 end
-0256 
-0257 %Begin writing species
-0258 for i=1:numel(model.mets)
-0259     %Add the default values, as these will be the same in all entries
-0260     if i==1
-0261         if isfield(modelSBML.species, 'sboTerm')
-0262             modelSBML.species(i).sboTerm=247;
-0263         end
-0264         if isfield(modelSBML.species, 'initialAmount')
-0265             modelSBML.species(i).initialAmount=1;
-0266         end
-0267         if isfield(modelSBML.species, 'initialConcentration')
-0268             modelSBML.species(i).initialConcentration=0;
-0269         end
-0270         if isfield(modelSBML.species, 'isSetInitialAmount')
-0271             modelSBML.species(i).isSetInitialAmount=1;
-0272         end
-0273         if isfield(modelSBML.species, 'isSetInitialConcentration')
-0274             modelSBML.species(i).isSetInitialConcentration=1;
-0275         end
-0276     end
-0277     %Copy the default values to the next entry as long as it is not the
-0278     %last one
-0279     if i<numel(model.mets)
-0280         modelSBML.species(i+1)=modelSBML.species(i);
-0281     end
-0282     
-0283     if isfield(modelSBML.species,'metaid')
-0284         modelSBML.species(i).metaid=['M_' model.mets{i}];
-0285     end
-0286     if isfield(modelSBML.species, 'name')
-0287         modelSBML.species(i).name=model.metNames{i};
-0288     end
-0289     if isfield(modelSBML.species, 'id')
-0290         modelSBML.species(i).id=['M_' model.mets{i}];
-0291     end
-0292     if isfield(modelSBML.species, 'compartment')
-0293         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
-0294     end
-0295     if isfield(model,'unconstrained')
-0296         if model.unconstrained(i)
-0297             modelSBML.species(i).boundaryCondition=1;
-0298         end
+0251     if ~isempty(model.compMiriams{i}) && isfield(modelSBML.compartment(i),'annotation')
+0252         modelSBML.compartment(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.comps{i} '">'];
+0253         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation '<bqbiol:is><rdf:Bag>'];
+0254         modelSBML.compartment(i).annotation=[modelSBML.compartment(i).annotation getMiriam(model.compMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0255     end
+0256     if isfield(modelSBML.compartment, 'name')
+0257         modelSBML.compartment(i).name=model.compNames{i};
+0258     end
+0259     if isfield(modelSBML.compartment, 'id')
+0260         modelSBML.compartment(i).id=model.comps{i};
+0261     end
+0262     
+0263 end
+0264 
+0265 %Begin writing species
+0266 for i=1:numel(model.mets)
+0267     %Add the default values, as these will be the same in all entries
+0268     if i==1
+0269         if isfield(modelSBML.species, 'sboTerm')
+0270             modelSBML.species(i).sboTerm=247;
+0271         end
+0272         if isfield(modelSBML.species, 'initialAmount')
+0273             modelSBML.species(i).initialAmount=1;
+0274         end
+0275         if isfield(modelSBML.species, 'initialConcentration')
+0276             modelSBML.species(i).initialConcentration=0;
+0277         end
+0278         if isfield(modelSBML.species, 'isSetInitialAmount')
+0279             modelSBML.species(i).isSetInitialAmount=1;
+0280         end
+0281         if isfield(modelSBML.species, 'isSetInitialConcentration')
+0282             modelSBML.species(i).isSetInitialConcentration=1;
+0283         end
+0284     end
+0285     %Copy the default values to the next entry as long as it is not the
+0286     %last one
+0287     if i<numel(model.mets)
+0288         modelSBML.species(i+1)=modelSBML.species(i);
+0289     end
+0290     
+0291     if isfield(modelSBML.species,'metaid')
+0292         modelSBML.species(i).metaid=['M_' model.mets{i}];
+0293     end
+0294     if isfield(modelSBML.species, 'name')
+0295         modelSBML.species(i).name=model.metNames{i};
+0296     end
+0297     if isfield(modelSBML.species, 'id')
+0298         modelSBML.species(i).id=['M_' model.mets{i}];
 0299     end
-0300     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
-0301         if ~isnan(model.metCharges(i))
-0302             modelSBML.species(i).fbc_charge=model.metCharges(i);
-0303             modelSBML.species(i).isSetfbc_charge=1;
-0304         else
-0305             modelSBML.species(i).isSetfbc_charge=0;
+0300     if isfield(modelSBML.species, 'compartment')
+0301         modelSBML.species(i).compartment=model.comps{model.metComps(i)};
+0302     end
+0303     if isfield(model,'unconstrained')
+0304         if model.unconstrained(i)
+0305             modelSBML.species(i).boundaryCondition=1;
 0306         end
 0307     end
-0308     if ~isempty(model.metMiriams{i})
-0309         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
-0310         if sbo_ind > 0
-0311             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0312             % remove the SBO term from metMiriams so the information is
-0313             % not duplicated in the "annotation" field later on
-0314             model.metMiriams{i}.name(sbo_ind) = [];
-0315             model.metMiriams{i}.value(sbo_ind) = [];
-0316         end
-0317     end
-0318     if isfield(modelSBML.species,'annotation')
-0319         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
-0320             hasInchi=false;
-0321             if ~isempty(model.metFormulas{i})
-0322                 %Only export formula if there is no InChI. This is because
-0323                 %the metFormulas field is populated by InChIs if available
-0324                 if ~isempty(model.inchis{i})
-0325                     hasInchi=true;
-0326                 end
-0327                 if hasInchi==false
-0328                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
-0329                 end
-0330             end
-0331             if ~isempty(model.metMiriams{i}) || hasInchi==true
-0332                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_M_' model.mets{i} '">'];
-0333                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
-0334                 if ~isempty(model.metMiriams{i})
-0335                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
-0336                 end
-0337                 if hasInchi==true
-0338                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
-0339                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
-0340                 end
-0341                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0342             end
-0343         end
-0344     end
-0345 end
-0346 
-0347 if isfield(model,'genes')
-0348     for i=1:numel(model.genes)
-0349         %Add the default values, as these will be the same in all entries
-0350         if i==1
-0351             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
-0352                 modelSBML.fbc_geneProduct(i).sboTerm=243;
-0353             end
-0354         end
-0355         %Copy the default values to the next index as long as it is not the
-0356         %last one
-0357         if i<numel(model.genes)
-0358             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
-0359         end
-0360         
-0361         if isfield(modelSBML.fbc_geneProduct,'metaid')
-0362             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
-0363         end
-0364         if ~isempty(model.geneMiriams{i})
-0365             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
-0366             if sbo_ind > 0
-0367                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0368                 % remove the SBO term from compMiriams so the information is
-0369                 % not duplicated in the "annotation" field later on
-0370                 model.geneMiriams{i}.name(sbo_ind) = [];
-0371                 model.geneMiriams{i}.value(sbo_ind) = [];
-0372             end
-0373         end
-0374         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
-0375             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
-0376             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
-0377             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0378         end
-0379         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
-0380             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
+0308     if isfield(modelSBML.species, 'fbc_charge') && isfield(model,'metCharges')
+0309         if ~isnan(model.metCharges(i))
+0310             modelSBML.species(i).fbc_charge=model.metCharges(i);
+0311             modelSBML.species(i).isSetfbc_charge=1;
+0312         else
+0313             modelSBML.species(i).isSetfbc_charge=0;
+0314         end
+0315     end
+0316     if ~isempty(model.metMiriams{i})
+0317         [~,sbo_ind] = ismember('sbo',model.metMiriams{i}.name);
+0318         if sbo_ind > 0
+0319             modelSBML.species(i).sboTerm=str2double(regexprep(model.metMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0320             % remove the SBO term from metMiriams so the information is
+0321             % not duplicated in the "annotation" field later on
+0322             model.metMiriams{i}.name(sbo_ind) = [];
+0323             model.metMiriams{i}.value(sbo_ind) = [];
+0324         end
+0325     end
+0326     if isfield(modelSBML.species,'annotation')
+0327         if ~isempty(model.metMiriams{i}) || ~isempty(model.metFormulas{i})
+0328             hasInchi=false;
+0329             if ~isempty(model.metFormulas{i})
+0330                 %Only export formula if there is no InChI. This is because
+0331                 %the metFormulas field is populated by InChIs if available
+0332                 if ~isempty(model.inchis{i})
+0333                     hasInchi=true;
+0334                 end
+0335                 if hasInchi==false
+0336                     modelSBML.species(i).fbc_chemicalFormula=model.metFormulas{i};
+0337                 end
+0338             end
+0339             if ~isempty(model.metMiriams{i}) || hasInchi==true
+0340                 modelSBML.species(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_M_' model.mets{i} '">'];
+0341                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<bqbiol:is><rdf:Bag>'];
+0342                 if ~isempty(model.metMiriams{i})
+0343                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation getMiriam(model.metMiriams{i})];
+0344                 end
+0345                 if hasInchi==true
+0346                     modelSBML.species(i).annotation=[modelSBML.species(i).annotation '<rdf:li rdf:resource="https://identifiers.org/inchi/InChI=' regexprep(model.inchis{i},'^InChI=','') '"/>'];
+0347                     modelSBML.species(i).fbc_chemicalFormula=char(regexp(model.inchis{i}, '/(\w+)/', 'tokens', 'once'));
+0348                 end
+0349                 modelSBML.species(i).annotation=[modelSBML.species(i).annotation '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0350             end
+0351         end
+0352     end
+0353 end
+0354 
+0355 if isfield(model,'genes')
+0356     for i=1:numel(model.genes)
+0357         %Add the default values, as these will be the same in all entries
+0358         if i==1
+0359             if isfield(modelSBML.fbc_geneProduct, 'sboTerm')
+0360                 modelSBML.fbc_geneProduct(i).sboTerm=243;
+0361             end
+0362         end
+0363         %Copy the default values to the next index as long as it is not the
+0364         %last one
+0365         if i<numel(model.genes)
+0366             modelSBML.fbc_geneProduct(i+1)=modelSBML.fbc_geneProduct(i);
+0367         end
+0368         
+0369         if isfield(modelSBML.fbc_geneProduct,'metaid')
+0370             modelSBML.fbc_geneProduct(i).metaid=model.genes{i};
+0371         end
+0372         if ~isempty(model.geneMiriams{i})
+0373             [~,sbo_ind] = ismember('sbo',model.geneMiriams{i}.name);
+0374             if sbo_ind > 0
+0375                 modelSBML.fbc_geneProduct(i).sboTerm=str2double(regexprep(model.geneMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0376                 % remove the SBO term from compMiriams so the information is
+0377                 % not duplicated in the "annotation" field later on
+0378                 model.geneMiriams{i}.name(sbo_ind) = [];
+0379                 model.geneMiriams{i}.value(sbo_ind) = [];
+0380             end
 0381         end
-0382         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
-0383             if isempty(model.geneShortNames{i})
-0384                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
-0385             else
-0386                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
-0387             end
-0388         end
-0389     end
-0390     if exportGeneComplexes==true
-0391         %Also add the complexes as genes. This is done by splitting grRules
-0392         %on "or" and adding the ones which contain several genes
-0393         geneComplexes={};
-0394         if isfield(model,'grRules')
-0395             %Only grRules which contain " and " can be complexes
-0396             uniqueRules=unique(model.grRules);
-0397             I=cellfun(@any,strfind(uniqueRules,' and '));
-0398             uniqueRules(~I)=[];
-0399             uniqueRules=strrep(uniqueRules,'(','');
-0400             uniqueRules=strrep(uniqueRules,')','');
-0401             uniqueRules=strrep(uniqueRules,' and ',':');
-0402             for i=1:numel(uniqueRules)
-0403                 genes=regexp(uniqueRules(i),' or ','split');
-0404                 genes=genes{1}(:);
-0405                 %Check which ones are complexes
-0406                 I=cellfun(@any,strfind(genes,':'));
-0407                 geneComplexes=[geneComplexes;genes(I)];
-0408             end
-0409         end
-0410         geneComplexes=unique(geneComplexes);
-0411         if ~isempty(geneComplexes)
-0412             %Then add them as genes. There is a possiblity that a complex
-0413             %A&B is added as separate from B&A. This is not really an issue
-0414             %so this is not dealt with
-0415             for i=1:numel(geneComplexes)
-0416                 modelSBML.fbc_geneProduct(numel(model.genes)+i)=modelSBML.fbc_geneProduct(1);
-0417                 if isfield(modelSBML.fbc_geneProduct,'metaid')
-0418                     modelSBML.fbc_geneProduct(numel(model.genes)+i).metaid=geneComplexes{i};
-0419                 end
-0420                 if isfield(modelSBML.fbc_geneProduct,'fbc_id')
-0421                     modelSBML.fbc_geneProduct(numel(model.genes)+i).fbc_id=geneComplexes{i};
-0422                 else
-0423                     modelSBML.fbc_geneProduct(i).fbc_label=modelSBML.fbc_geneProduct(i).fbc_id;
-0424                 end
-0425             end
-0426         end
-0427     end
-0428 end
-0429 
-0430 %Generate a list of unique fbc_bound names
-0431 totalValues=[model.lb; model.ub];
-0432 totalNames=cell(size(totalValues,1),1);
-0433 
-0434 listUniqueValues=unique(totalValues);
-0435 
-0436 for i=1:length(listUniqueValues)
-0437     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
-0438     ind=find(ismember(totalValues,listUniqueValues(i)));
-0439     totalNames(ind)=listUniqueNames(i,1);
-0440 end
+0382         if ~isempty(model.geneMiriams{i}) && isfield(modelSBML.fbc_geneProduct(i),'annotation')
+0383             modelSBML.fbc_geneProduct(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_' model.genes{i} '">'];
+0384             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation '<bqbiol:is><rdf:Bag>'];
+0385             modelSBML.fbc_geneProduct(i).annotation=[modelSBML.fbc_geneProduct(i).annotation getMiriam(model.geneMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0386         end
+0387         if isfield(modelSBML.fbc_geneProduct, 'fbc_id')
+0388             modelSBML.fbc_geneProduct(i).fbc_id=model.genes{i};
+0389         end
+0390         if isfield(modelSBML.fbc_geneProduct, 'fbc_label') && isfield(model,'geneShortNames')
+0391             if isempty(model.geneShortNames{i})
+0392                 modelSBML.fbc_geneProduct(i).fbc_label=model.genes{i};
+0393             else
+0394                 modelSBML.fbc_geneProduct(i).fbc_label=model.geneShortNames{i};
+0395             end
+0396         end
+0397     end
+0398     if exportGeneComplexes==true
+0399         %Also add the complexes as genes. This is done by splitting grRules
+0400         %on "or" and adding the ones which contain several genes
+0401         geneComplexes={};
+0402         if isfield(model,'grRules')
+0403             %Only grRules which contain " and " can be complexes
+0404             uniqueRules=unique(model.grRules);
+0405             I=cellfun(@any,strfind(uniqueRules,' and '));
+0406             uniqueRules(~I)=[];
+0407             uniqueRules=strrep(uniqueRules,'(','');
+0408             uniqueRules=strrep(uniqueRules,')','');
+0409             uniqueRules=strrep(uniqueRules,' and ',':');
+0410             for i=1:numel(uniqueRules)
+0411                 genes=regexp(uniqueRules(i),' or ','split');
+0412                 genes=genes{1}(:);
+0413                 %Check which ones are complexes
+0414                 I=cellfun(@any,strfind(genes,':'));
+0415                 geneComplexes=[geneComplexes;genes(I)];
+0416             end
+0417         end
+0418         geneComplexes=unique(geneComplexes);
+0419         if ~isempty(geneComplexes)
+0420             %Then add them as genes. There is a possiblity that a complex
+0421             %A&B is added as separate from B&A. This is not really an issue
+0422             %so this is not dealt with
+0423             for i=1:numel(geneComplexes)
+0424                 modelSBML.fbc_geneProduct(numel(model.genes)+i)=modelSBML.fbc_geneProduct(1);
+0425                 if isfield(modelSBML.fbc_geneProduct,'metaid')
+0426                     modelSBML.fbc_geneProduct(numel(model.genes)+i).metaid=geneComplexes{i};
+0427                 end
+0428                 if isfield(modelSBML.fbc_geneProduct,'fbc_id')
+0429                     modelSBML.fbc_geneProduct(numel(model.genes)+i).fbc_id=geneComplexes{i};
+0430                 else
+0431                     modelSBML.fbc_geneProduct(i).fbc_label=modelSBML.fbc_geneProduct(i).fbc_id;
+0432                 end
+0433             end
+0434         end
+0435     end
+0436 end
+0437 
+0438 %Generate a list of unique fbc_bound names
+0439 totalValues=[model.lb; model.ub];
+0440 totalNames=cell(size(totalValues,1),1);
 0441 
-0442 for i=1:length(listUniqueNames)
-0443     %Add the default values, as these will be the same in all entries
-0444     if i==1
-0445         if isfield(modelSBML.parameter, 'constant')
-0446             modelSBML.parameter(i).constant=1;
-0447         end
-0448         if isfield(modelSBML.parameter, 'isSetValue')
-0449             modelSBML.parameter(i).isSetValue=1;
-0450         end
-0451     end
-0452     %Copy the default values to the next index as long as it is not the
-0453     %last one
-0454     if i<numel(listUniqueNames)
-0455         modelSBML.parameter(i+1)=modelSBML.parameter(i);
-0456     end
-0457     modelSBML.parameter(i).id=listUniqueNames{i};
-0458     modelSBML.parameter(i).value=listUniqueValues(i);
-0459 end
-0460 
-0461 for i=1:numel(model.rxns)
-0462     %Add the default values, as these will be the same in all entries
-0463     if i==1
-0464         if isfield(modelSBML.reaction, 'sboTerm')
-0465             modelSBML.reaction(i).sboTerm=176;
-0466         end
-0467         if isfield(modelSBML.reaction, 'isSetFast')
-0468             modelSBML.reaction(i).isSetFast=1;
-0469         end
-0470     end
-0471     %Copy the default values to the next index as long as it is not the
-0472     %last one
-0473     if i<numel(model.rxns)
-0474         modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0475     end
-0476     
-0477     if isfield(modelSBML.reaction,'metaid')
-0478         modelSBML.reaction(i).metaid=['R_' model.rxns{i}];
-0479     end
-0480     
-0481     %Export notes information
-0482     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
-0483         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
-0484         if ~isnan(model.rxnConfidenceScores(i))
-0485             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
-0486         end
-0487         if ~isempty(model.rxnReferences{i})
-0488             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
-0489         end
-0490         if ~isempty(model.rxnNotes{i})
-0491             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
-0492         end
-0493         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
-0494     end
-0495     
-0496     % Export SBO terms from rxnMiriams
-0497     if ~isempty(model.rxnMiriams{i})
-0498         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
-0499         if sbo_ind > 0
-0500             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
-0501             % remove the SBO term from rxnMiriams so the information is not
-0502             % duplicated in the "annotation" field later on
-0503             model.rxnMiriams{i}.name(sbo_ind) = [];
-0504             model.rxnMiriams{i}.value(sbo_ind) = [];
-0505         end
-0506     end
-0507     
-0508     %Export annotation information from rxnMiriams
-0509     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
-0510         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_R_' model.rxns{i} '">'];
-0511         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
-0512         if ~isempty(model.eccodes{i})
-0513             eccodes=regexp(model.eccodes{i},';','split');
-0514             for j=1:numel(eccodes)
-0515                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
-0516             end
-0517         end
-0518         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
-0519     end
-0520     
-0521     if isfield(modelSBML.reaction, 'name')
-0522         modelSBML.reaction(i).name=model.rxnNames{i};
-0523     end
-0524     if isfield(modelSBML.reaction, 'id')
-0525         modelSBML.reaction(i).id=['R_' model.rxns{i}];
-0526     end
-0527     
-0528     %Add the information about reactants and products
-0529     involvedMets=addReactantsProducts(model,modelSBML,i);
-0530     for j=1:numel(involvedMets.reactant)
-0531         if j<numel(involvedMets.reactant)
-0532             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
-0533         end
-0534         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
-0535         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
-0536         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
-0537         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
-0538     end
-0539     if numel(involvedMets.reactant)==0
-0540         modelSBML.reaction(i).reactant='';
-0541     end
-0542     for j=1:numel(involvedMets.product)
-0543         if j<numel(involvedMets.product)
-0544             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
-0545         end
-0546         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
-0547         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
-0548         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
-0549         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
-0550     end
-0551     if numel(involvedMets.product)==0
-0552         modelSBML.reaction(i).product='';
-0553     end
-0554     %Export reversibility information. Reactions are irreversible by
-0555     %default
-0556     if model.rev(i)==1
-0557         modelSBML.reaction(i).reversible=1;
+0442 listUniqueValues=unique(totalValues);
+0443 
+0444 for i=1:length(listUniqueValues)
+0445     listUniqueNames{i,1}=['FB',num2str(i),'N',num2str(abs(round(listUniqueValues(i))))]; % create unique flux bound IDs.
+0446     ind=find(ismember(totalValues,listUniqueValues(i)));
+0447     totalNames(ind)=listUniqueNames(i,1);
+0448 end
+0449 
+0450 for i=1:length(listUniqueNames)
+0451     %Add the default values, as these will be the same in all entries
+0452     if i==1
+0453         if isfield(modelSBML.parameter, 'constant')
+0454             modelSBML.parameter(i).constant=1;
+0455         end
+0456         if isfield(modelSBML.parameter, 'isSetValue')
+0457             modelSBML.parameter(i).isSetValue=1;
+0458         end
+0459     end
+0460     %Copy the default values to the next index as long as it is not the
+0461     %last one
+0462     if i<numel(listUniqueNames)
+0463         modelSBML.parameter(i+1)=modelSBML.parameter(i);
+0464     end
+0465     modelSBML.parameter(i).id=listUniqueNames{i};
+0466     modelSBML.parameter(i).value=listUniqueValues(i);
+0467 end
+0468 
+0469 for i=1:numel(model.rxns)
+0470     %Add the default values, as these will be the same in all entries
+0471     if i==1
+0472         if isfield(modelSBML.reaction, 'sboTerm')
+0473             modelSBML.reaction(i).sboTerm=176;
+0474         end
+0475         if isfield(modelSBML.reaction, 'isSetFast')
+0476             modelSBML.reaction(i).isSetFast=1;
+0477         end
+0478     end
+0479     %Copy the default values to the next index as long as it is not the
+0480     %last one
+0481     if i<numel(model.rxns)
+0482         modelSBML.reaction(i+1)=modelSBML.reaction(i);
+0483     end
+0484     
+0485     if isfield(modelSBML.reaction,'metaid')
+0486         modelSBML.reaction(i).metaid=['R_' model.rxns{i}];
+0487     end
+0488     
+0489     %Export notes information
+0490     if (~isnan(model.rxnConfidenceScores(i)) || ~isempty(model.rxnReferences{i}) || ~isempty(model.rxnNotes{i}))
+0491         modelSBML.reaction(i).notes='<notes><body xmlns="http://www.w3.org/1999/xhtml">';
+0492         if ~isnan(model.rxnConfidenceScores(i))
+0493             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>Confidence Level: ' num2str(model.rxnConfidenceScores(i)) '</p>'];
+0494         end
+0495         if ~isempty(model.rxnReferences{i})
+0496             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>AUTHORS: ' model.rxnReferences{i} '</p>'];
+0497         end
+0498         if ~isempty(model.rxnNotes{i})
+0499             modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '<p>NOTES: ' model.rxnNotes{i} '</p>'];
+0500         end
+0501         modelSBML.reaction(i).notes=[modelSBML.reaction(i).notes '</body></notes>'];
+0502     end
+0503     
+0504     % Export SBO terms from rxnMiriams
+0505     if ~isempty(model.rxnMiriams{i})
+0506         [~,sbo_ind] = ismember('sbo',model.rxnMiriams{i}.name);
+0507         if sbo_ind > 0
+0508             modelSBML.reaction(i).sboTerm=str2double(regexprep(model.rxnMiriams{i}.value{sbo_ind},'SBO:','','ignorecase'));
+0509             % remove the SBO term from rxnMiriams so the information is not
+0510             % duplicated in the "annotation" field later on
+0511             model.rxnMiriams{i}.name(sbo_ind) = [];
+0512             model.rxnMiriams{i}.value(sbo_ind) = [];
+0513         end
+0514     end
+0515     
+0516     %Export annotation information from rxnMiriams
+0517     if (~isempty(model.rxnMiriams{i}) && isfield(modelSBML.reaction(i),'annotation')) || ~isempty(model.eccodes{i})
+0518         modelSBML.reaction(i).annotation=['<annotation><rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/"><rdf:Description rdf:about="#meta_R_' model.rxns{i} '">'];
+0519         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation '<bqbiol:is><rdf:Bag>'];
+0520         if ~isempty(model.eccodes{i})
+0521             eccodes=regexp(model.eccodes{i},';','split');
+0522             for j=1:numel(eccodes)
+0523                 modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation  '<rdf:li rdf:resource="https://identifiers.org/ec-code/' regexprep(eccodes{j},'ec-code/|EC','') '"/>'];
+0524             end
+0525         end
+0526         modelSBML.reaction(i).annotation=[modelSBML.reaction(i).annotation getMiriam(model.rxnMiriams{i}) '</rdf:Bag></bqbiol:is></rdf:Description></rdf:RDF></annotation>'];
+0527     end
+0528     
+0529     if isfield(modelSBML.reaction, 'name')
+0530         modelSBML.reaction(i).name=model.rxnNames{i};
+0531     end
+0532     if isfield(modelSBML.reaction, 'id')
+0533         modelSBML.reaction(i).id=['R_' model.rxns{i}];
+0534     end
+0535     
+0536     %Add the information about reactants and products
+0537     involvedMets=addReactantsProducts(model,modelSBML,i);
+0538     for j=1:numel(involvedMets.reactant)
+0539         if j<numel(involvedMets.reactant)
+0540             modelSBML.reaction(i).reactant(j+1)=modelSBML.reaction(i).reactant(j);
+0541         end
+0542         modelSBML.reaction(i).reactant(j).species=involvedMets.reactant(j).species;
+0543         modelSBML.reaction(i).reactant(j).stoichiometry=involvedMets.reactant(j).stoichiometry;
+0544         modelSBML.reaction(i).reactant(j).isSetStoichiometry=involvedMets.reactant(j).isSetStoichiometry;
+0545         modelSBML.reaction(i).reactant(j).constant=involvedMets.reactant(j).constant;
+0546     end
+0547     if numel(involvedMets.reactant)==0
+0548         modelSBML.reaction(i).reactant='';
+0549     end
+0550     for j=1:numel(involvedMets.product)
+0551         if j<numel(involvedMets.product)
+0552             modelSBML.reaction(i).product(j+1)=modelSBML.reaction(i).product(j);
+0553         end
+0554         modelSBML.reaction(i).product(j).species=involvedMets.product(j).species;
+0555         modelSBML.reaction(i).product(j).stoichiometry=involvedMets.product(j).stoichiometry;
+0556         modelSBML.reaction(i).product(j).isSetStoichiometry=involvedMets.product(j).isSetStoichiometry;
+0557         modelSBML.reaction(i).product(j).constant=involvedMets.product(j).constant;
 0558     end
-0559     if isfield(model, 'rxnComps')
-0560         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
+0559     if numel(involvedMets.product)==0
+0560         modelSBML.reaction(i).product='';
 0561     end
-0562     if isfield(model, 'grRules')
-0563         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
-0564     end
-0565     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
-0566     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
-0567 end
-0568 
-0569 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
-0570 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
-0571 %license file in readme/GPL.MD. Code modified for RAVEN
-0572 if modelHasSubsystems
-0573     modelSBML.groups_group.groups_kind = 'partonomy';
-0574     modelSBML.groups_group.sboTerm = 633;
-0575     tmpStruct=modelSBML.groups_group;
+0562     %Export reversibility information. Reactions are irreversible by
+0563     %default
+0564     if model.rev(i)==1
+0565         modelSBML.reaction(i).reversible=1;
+0566     end
+0567     if isfield(model, 'rxnComps')
+0568         modelSBML.reaction(i).compartment=model.comps{model.rxnComps(i)};
+0569     end
+0570     if isfield(model, 'grRules')
+0571         modelSBML.reaction(i).fbc_geneProductAssociation.fbc_association.fbc_association=model.grRules{i};
+0572     end
+0573     modelSBML.reaction(i).fbc_lowerFluxBound=totalNames{i};
+0574     modelSBML.reaction(i).fbc_upperFluxBound=totalNames{length(model.lb)+i};
+0575 end
 0576 
-0577     rxns=strcat('R_',model.rxns);
-0578     if ~any(cellfun(@iscell,model.subSystems))
-0579         if ~any(~cellfun(@isempty,model.subSystems))
-0580             subSystems = {};
-0581         else
-0582             subSystems = setdiff(model.subSystems,'');
-0583         end
-0584     else
-0585         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
-0586         subSystems = setdiff(vertcat(orderedSubs{:}),'');
-0587     end
-0588     if isempty(subSystems)
-0589         subSystems = {};
-0590     end
-0591     if ~isempty(subSystems)
-0592         %Build the groups for the group package
-0593         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
-0594         for i = 1:length(subSystems)
-0595             cgroup = tmpStruct;
-0596             if ~any(cellfun(@iscell,model.subSystems))
-0597                 present = ismember(model.subSystems,subSystems{i});
-0598             else
-0599                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
-0600             end
-0601             groupMembers = rxns(present);
-0602             for j = 1:numel(groupMembers)
-0603                 cMember = tmpStruct.groups_member;
-0604                 cMember.groups_idRef = groupMembers{j};
-0605                 if j == 1
-0606                     cgroup.groups_member = cMember;
-0607                 else
-0608                     cgroup.groups_member(j) = cMember;
-0609                 end
-0610             end
-0611             cgroup.groups_id = groupIDs{i};
-0612             cgroup.groups_name = subSystems{i};
-0613             if i == 1
-0614                 modelSBML.groups_group = cgroup;
-0615             else
-0616                 modelSBML.groups_group(i) = cgroup;
-0617             end
-0618         end
-0619     end
-0620 end
-0621 
-0622 %Prepare fbc_objective subfield
-0623 
-0624 modelSBML.fbc_objective.fbc_type='maximize';
-0625 modelSBML.fbc_objective.fbc_id='obj';
-0626 
-0627 ind=find(model.c);
-0628 
-0629 if isempty(ind)
-0630     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
-0631     EM='The objective function is not defined. The model will be exported as it is. Notice that having undefined objective function may produce warnings related to "fbc:coefficient" and "fbc:reaction" in SBML Validator';
-0632     dispEM(EM,false);
-0633 else
-0634     for i=1:length(ind)
-0635         %Copy the default values to the next index as long as it is not the
-0636         %last one
-0637         if i<numel(ind)
-0638             modelSBML.reaction(i+1)=modelSBML.reaction(i);
-0639         end
-0640         values=model.c(model.c~=0);
-0641         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
-0642         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
-0643         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
-0644     end
-0645 end
-0646 
-0647 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
-0648 
-0649 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
-0650 if modelHasSubsystems
-0651     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
-0652     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
-0653     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0654     fbcStr,groupStr});
-0655 else
-0656     modelSBML.namespaces=struct('prefix',{'','fbc'},...
-0657     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
-0658     fbcStr});
-0659 end
-0660 
-0661 if sbmlPackageVersions(1) == 2
-0662     modelSBML.fbc_strict=1;
-0663 end
-0664 
-0665 modelSBML.rule=[];
-0666 modelSBML.constraint=[];
-0667 
-0668 OutputSBML(modelSBML,fileName,1,0,[1,0]);
-0669 end
-0670 
-0671 
-0672 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
-0673 %Returns the blank SBML model structure by using appropriate libSBML
-0674 %functions. This creates structure by considering three levels
+0577 %Prepare subSystems Code taken from COBRA functions getModelSubSystems,
+0578 %writeSBML, findRxnsFromSubSystem under GNU General Public License v3.0,
+0579 %license file in readme/GPL.MD. Code modified for RAVEN
+0580 if modelHasSubsystems
+0581     modelSBML.groups_group.groups_kind = 'partonomy';
+0582     modelSBML.groups_group.sboTerm = 633;
+0583     tmpStruct=modelSBML.groups_group;
+0584 
+0585     rxns=strcat('R_',model.rxns);
+0586     if ~any(cellfun(@iscell,model.subSystems))
+0587         if ~any(~cellfun(@isempty,model.subSystems))
+0588             subSystems = {};
+0589         else
+0590             subSystems = setdiff(model.subSystems,'');
+0591         end
+0592     else
+0593         orderedSubs = cellfun(@(x) columnVector(x),model.subSystems,'UniformOUtput',false);
+0594         subSystems = setdiff(vertcat(orderedSubs{:}),'');
+0595     end
+0596     if isempty(subSystems)
+0597         subSystems = {};
+0598     end
+0599     if ~isempty(subSystems)
+0600         %Build the groups for the group package
+0601         groupIDs = strcat('group',cellfun(@num2str, num2cell(1:length(subSystems)),'UniformOutput',false));
+0602         for i = 1:length(subSystems)
+0603             cgroup = tmpStruct;
+0604             if ~any(cellfun(@iscell,model.subSystems))
+0605                 present = ismember(model.subSystems,subSystems{i});
+0606             else
+0607                 present = cellfun(@(x) any(ismember(x,subSystems{i})),model.subSystems);
+0608             end
+0609             groupMembers = rxns(present);
+0610             for j = 1:numel(groupMembers)
+0611                 cMember = tmpStruct.groups_member;
+0612                 cMember.groups_idRef = groupMembers{j};
+0613                 if j == 1
+0614                     cgroup.groups_member = cMember;
+0615                 else
+0616                     cgroup.groups_member(j) = cMember;
+0617                 end
+0618             end
+0619             cgroup.groups_id = groupIDs{i};
+0620             cgroup.groups_name = subSystems{i};
+0621             if i == 1
+0622                 modelSBML.groups_group = cgroup;
+0623             else
+0624                 modelSBML.groups_group(i) = cgroup;
+0625             end
+0626         end
+0627     end
+0628 end
+0629 
+0630 %Prepare fbc_objective subfield
+0631 
+0632 modelSBML.fbc_objective.fbc_type='maximize';
+0633 modelSBML.fbc_objective.fbc_id='obj';
+0634 
+0635 ind=find(model.c);
+0636 
+0637 if isempty(ind)
+0638     modelSBML.fbc_objective.fbc_fluxObjective.fbc_coefficient=0;
+0639     EM='The objective function is not defined. The model will be exported as it is. Notice that having undefined objective function may produce warnings related to "fbc:coefficient" and "fbc:reaction" in SBML Validator';
+0640     dispEM(EM,false);
+0641 else
+0642     for i=1:length(ind)
+0643         %Copy the default values to the next index as long as it is not the
+0644         %last one
+0645         if i<numel(ind)
+0646             modelSBML.reaction(i+1)=modelSBML.reaction(i);
+0647         end
+0648         values=model.c(model.c~=0);
+0649         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_reaction=modelSBML.reaction(ind(i)).id;
+0650         modelSBML.fbc_objective(i).fbc_fluxObjective.fbc_coefficient=values(i);
+0651         modelSBML.fbc_objective(i).fbc_fluxObjective.isSetfbc_coefficient=1;
+0652     end
+0653 end
+0654 
+0655 modelSBML.fbc_activeObjective=modelSBML.fbc_objective.fbc_id;
+0656 
+0657 fbcStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/fbc/version',num2str(sbmlPackageVersions(1))];
+0658 if modelHasSubsystems
+0659     groupStr=['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/groups/version',num2str(sbmlPackageVersions(2))];
+0660     modelSBML.namespaces=struct('prefix',{'','fbc','groups'},...
+0661     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0662     fbcStr,groupStr});
+0663 else
+0664     modelSBML.namespaces=struct('prefix',{'','fbc'},...
+0665     'uri',{['http://www.sbml.org/sbml/level', num2str(sbmlLevel), '/version', num2str(sbmlVersion), '/core'],...
+0666     fbcStr});
+0667 end
+0668 
+0669 if sbmlPackageVersions(1) == 2
+0670     modelSBML.fbc_strict=1;
+0671 end
+0672 
+0673 modelSBML.rule=[];
+0674 modelSBML.constraint=[];
 0675 
-0676 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0677 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0676 OutputSBML(modelSBML,fileName,1,0,[1,0]);
+0677 end
 0678 
-0679 for i=1:numel(sbmlFieldNames)
-0680     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0681     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0682     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0683     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
-0684         for j=1:numel(sbmlSubfieldNames)
-0685             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
-0686             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0687             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0688             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
-0689                 for k=1:numel(sbmlSubsubfieldNames)
-0690                     %'compartment' and 'species' fields are not supposed to
-0691                     %have their standalone structures if they are subfields
-0692                     %or subsubfields
-0693                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
-0694                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
-0695                     end
-0696                     %If it is fbc_association in the third level, we need
-0697                     %to establish the fourth level, since libSBML requires
-0698                     %it
-0699                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
-0700                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0701                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0702                         for l=1:numel(fbc_associationFieldNames)
-0703                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
-0704                         end
-0705                     end
-0706                 end
-0707             end
-0708         end
-0709     end
-0710     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
-0711         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
-0712     end
-0713 end
-0714 
-0715 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
-0716 
-0717 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0718 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
-0719 
-0720 kinds={'mole','gram','second'};
-0721 exponents=[1 -1 -1];
-0722 scales=[-3 0 0];
-0723 multipliers=[1 1 1*60*60];
+0679 
+0680 function modelSBML=getSBMLStructure(sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions)
+0681 %Returns the blank SBML model structure by using appropriate libSBML
+0682 %functions. This creates structure by considering three levels
+0683 
+0684 sbmlFieldNames=getStructureFieldnames('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0685 sbmlDefaultValues=getDefaultValues('model',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0686 
+0687 for i=1:numel(sbmlFieldNames)
+0688     modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0689     sbmlSubfieldNames=getStructureFieldnames(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0690     sbmlSubfieldValues=getDefaultValues(sbmlFieldNames{1,i},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0691     if ~strcmp(sbmlFieldNames{1,i},'event') && ~strcmp(sbmlFieldNames{1,i},'functionDefinition') && ~strcmp(sbmlFieldNames{1,i},'initialAssignment')
+0692         for j=1:numel(sbmlSubfieldNames)
+0693             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j})=sbmlSubfieldValues{1,j};
+0694             sbmlSubsubfieldNames=getStructureFieldnames(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0695             sbmlSubsubfieldValues=getDefaultValues(sbmlSubfieldNames{1,j},sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0696             if ~strcmp(sbmlSubfieldNames{1,j},'modifier') && ~strcmp(sbmlSubfieldNames{1,j},'kineticLaw')
+0697                 for k=1:numel(sbmlSubsubfieldNames)
+0698                     %'compartment' and 'species' fields are not supposed to
+0699                     %have their standalone structures if they are subfields
+0700                     %or subsubfields
+0701                     if ~strcmp(sbmlSubfieldNames{1,j},'compartment') && ~strcmp(sbmlSubfieldNames{1,j},'species')
+0702                         modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k})=sbmlSubsubfieldValues{1,k};
+0703                     end
+0704                     %If it is fbc_association in the third level, we need
+0705                     %to establish the fourth level, since libSBML requires
+0706                     %it
+0707                     if strcmp(sbmlSubsubfieldNames{1,k},'fbc_association')
+0708                         fbc_associationFieldNames=getStructureFieldnames('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0709                         fbc_associationFieldValues=getDefaultValues('fbc_association',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0710                         for l=1:numel(fbc_associationFieldNames)
+0711                             modelSBML.(sbmlFieldNames{1,i}).(sbmlSubfieldNames{1,j}).(sbmlSubsubfieldNames{1,k}).(fbc_associationFieldNames{1,l})=fbc_associationFieldValues{1,l};
+0712                         end
+0713                     end
+0714                 end
+0715             end
+0716         end
+0717     end
+0718     if ~isstruct(modelSBML.(sbmlFieldNames{1,i}))
+0719         modelSBML.(sbmlFieldNames{1,i})=sbmlDefaultValues{1,i};
+0720     end
+0721 end
+0722 
+0723 modelSBML.unitDefinition.id='mmol_per_gDW_per_hr';
 0724 
-0725 for i=1:numel(unitFieldNames)
-0726     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0727     for j=1:3
-0728         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
-0729         if strcmp(unitFieldNames{1,i},'kind')
-0730             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
-0731         elseif strcmp(unitFieldNames{1,i},'exponent')
-0732             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
-0733         elseif strcmp(unitFieldNames{1,i},'scale')
-0734             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
-0735         elseif strcmp(unitFieldNames{1,i},'multiplier')
-0736             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
-0737         end
-0738     end
-0739 end
-0740 end
-0741 
-0742 function miriamString=getMiriam(miriamStruct)
-0743 %Returns a string with list elements for a miriam structure ('<rdf:li
-0744 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
-0745 %is just to speed up things since this is done many times during the
-0746 %exporting
-0747 
-0748 miriamString='';
-0749 if isfield(miriamStruct,'name')
-0750     for i=1:numel(miriamStruct.name)
-0751         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
-0752     end
-0753 end
-0754 end
+0725 unitFieldNames=getStructureFieldnames('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0726 unitDefaultValues=getDefaultValues('unit',sbmlLevel,sbmlVersion,sbmlPackages,sbmlPackageVersions);
+0727 
+0728 kinds={'mole','gram','second'};
+0729 exponents=[1 -1 -1];
+0730 scales=[-3 0 0];
+0731 multipliers=[1 1 1*60*60];
+0732 
+0733 for i=1:numel(unitFieldNames)
+0734     modelSBML.unitDefinition.unit(1).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0735     for j=1:3
+0736         modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=unitDefaultValues{1,i};
+0737         if strcmp(unitFieldNames{1,i},'kind')
+0738             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=kinds{j};
+0739         elseif strcmp(unitFieldNames{1,i},'exponent')
+0740             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=exponents(j);
+0741         elseif strcmp(unitFieldNames{1,i},'scale')
+0742             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=scales(j);
+0743         elseif strcmp(unitFieldNames{1,i},'multiplier')
+0744             modelSBML.unitDefinition.unit(j).(unitFieldNames{1,i})=multipliers(j);
+0745         end
+0746     end
+0747 end
+0748 end
+0749 
+0750 function miriamString=getMiriam(miriamStruct)
+0751 %Returns a string with list elements for a miriam structure ('<rdf:li
+0752 %rdf:resource="https://identifiers.org/go/GO:0005739"/>' for example). This
+0753 %is just to speed up things since this is done many times during the
+0754 %exporting
 0755 
-0756 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
-0757 %This function provides reactants and products for particular reaction. The
-0758 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
-0759 
-0760 met_idx = find(model.S(:, i));
-0761 tmp_Rxn.product=[];
-0762 tmp_Rxn.reactant=[];
-0763 for j_met=1:size(met_idx,1)
-0764     tmp_idx = met_idx(j_met,1);
-0765     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
-0766     met_stoich = model.S(tmp_idx, i);
-0767     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
-0768     sbml_tmp_species_ref.isSetStoichiometry=1;
-0769     sbml_tmp_species_ref.constant=1;
-0770     if (met_stoich > 0)
-0771         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
-0772     else
-0773         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
-0774     end
-0775 end
-0776 end
-0777 
-0778 function vecT = columnVector(vec)
-0779 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
-0780 % license file in readme/GPL.MD.
-0781 %
-0782 % Converts a vector to a column vector
-0783 %
-0784 % USAGE:
-0785 %
-0786 %   vecT = columnVector(vec)
-0787 %
-0788 % INPUT:
-0789 %   vec:     a vector
-0790 %
-0791 % OUTPUT:
-0792 %   vecT:    a column vector
-0793 
-0794 [n, m] = size(vec);
-0795 
-0796 if n < m
-0797     vecT = vec';
-0798 else
-0799     vecT = vec;
-0800 end
-0801 end
    
+0756 miriamString='';
+0757 if isfield(miriamStruct,'name')
+0758     for i=1:numel(miriamStruct.name)
+0759         miriamString=[miriamString '<rdf:li rdf:resource="https://identifiers.org/' miriamStruct.name{i} '/' miriamStruct.value{i} '"/>'];
+0760     end
+0761 end
+0762 end
+0763 
+0764 function [tmp_Rxn]=addReactantsProducts(model,sbmlModel,i)
+0765 %This function provides reactants and products for particular reaction. The
+0766 %function was 'borrowed' from writeSBML in COBRA toolbox, lines 663-679
+0767 
+0768 met_idx = find(model.S(:, i));
+0769 tmp_Rxn.product=[];
+0770 tmp_Rxn.reactant=[];
+0771 for j_met=1:size(met_idx,1)
+0772     tmp_idx = met_idx(j_met,1);
+0773     sbml_tmp_species_ref.species = sbmlModel.species(tmp_idx).id;
+0774     met_stoich = model.S(tmp_idx, i);
+0775     sbml_tmp_species_ref.stoichiometry = abs(met_stoich);
+0776     sbml_tmp_species_ref.isSetStoichiometry=1;
+0777     sbml_tmp_species_ref.constant=1;
+0778     if (met_stoich > 0)
+0779         tmp_Rxn.product = [ tmp_Rxn.product, sbml_tmp_species_ref ];
+0780     else
+0781         tmp_Rxn.reactant = [ tmp_Rxn.reactant, sbml_tmp_species_ref];
+0782     end
+0783 end
+0784 end
+0785 
+0786 function vecT = columnVector(vec)
+0787 % Code below taken from COBRA Toolbox under GNU General Public License v3.0
+0788 % license file in readme/GPL.MD.
+0789 %
+0790 % Converts a vector to a column vector
+0791 %
+0792 % USAGE:
+0793 %
+0794 %   vecT = columnVector(vec)
+0795 %
+0796 % INPUT:
+0797 %   vec:     a vector
+0798 %
+0799 % OUTPUT:
+0800 %   vecT:    a column vector
+0801 
+0802 [n, m] = size(vec);
+0803 
+0804 if n < m
+0805     vecT = vec';
+0806 else
+0807     vecT = vec;
+0808 end
+0809 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportToExcelFormat.html b/doc/io/exportToExcelFormat.html
index df284072..35004a4e 100644
--- a/doc/io/exportToExcelFormat.html
+++ b/doc/io/exportToExcelFormat.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportToExcelFormat

    SYNOPSIS ^

    -
    function exportToExcelFormat(model,filename)
    +
    function exportToExcelFormat(model,filename,sortIds)

    DESCRIPTION ^

     exportToExcelFormat
@@ -36,6 +36,9 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • exportToTabDelimited	exportToTabDelimited
  • loadWorkbook	loadWorkbook
  • sortIdentifiers	exportModel
  • writeSheet	writeSheet
    • 
 This function is called by:
 
+
  • exportForGit	exportForGit
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function exportToExcelFormat(model,filename)
+
    0001 function exportToExcelFormat(model,filename,sortIds)
 0002 % exportToExcelFormat
 0003 %   Exports a model structure to the Microsoft Excel model format
 0004 %
@@ -68,369 +71,378 @@ 
    SOURCE CODE ^%               be only a path, in which case the model is exported to a set
 0009 %               of tab-delimited text files instead. See exportToTabDelimited
 0010 %               for details regarding that functionality
-0011 %
-0012 %   The resulting Excel file can be used with importExcelModel/SBMLFromExcel
-0013 %   for modelling or to generate a SBML file.
+0011 %   sortIds     logical whether metabolites, reactions and genes should be
+0012 %               sorted alphabetically by their identifiers (opt, default
+0013 %               false)
 0014 %
-0015 %   NOTE: No checks are made regarding the correctness of the model. Use
-0016 %         checkModelStruct to identify problems in the model structure
+0015 %   The resulting Excel file can be used with importExcelModel/SBMLFromExcel
+0016 %   for modelling or to generate a SBML file.
 0017 %
-0018 %   Usage: exportToExcelFormat(model,filename)
-0019 
-0020 [~, A, B]=fileparts(filename);
-0021 
-0022 %If a path was used call on exportToTabDelimited instead
-0023 if ~any(A) || ~any(B)
-0024     exportToTabDelimited(model,filename);
-0025     return;
-0026 end
-0027 
-0028 if ~strcmpi(B,'.xlsx')
-0029     EM='As of RAVEN version 1.9, only export to xlsx format is supported';
-0030     dispEM(EM);
-0031 end
-0032 
-0033 import java.io.File;
-0034 import java.io.FileOutputStream;
-0035 import java.io.IOException;
+0018 %   NOTE: No checks are made regarding the correctness of the model. Use
+0019 %         checkModelStruct to identify problems in the model structure
+0020 %
+0021 %   Usage: exportToExcelFormat(model,filename,sortIds)
+0022 if nargin<3
+0023     sortIds=false;
+0024 end
+0025 if sortIds==true
+0026     model=sortIdentifiers(model);
+0027 end
+0028 
+0029 [~, A, B]=fileparts(filename);
+0030 
+0031 %If a path was used call on exportToTabDelimited instead
+0032 if ~any(A) || ~any(B)
+0033     exportToTabDelimited(model,filename);
+0034     return;
+0035 end
 0036 
-0037 %Remove the output file if it already exists
-0038 if exist(filename,'file')
-0039     delete(filename);
+0037 if ~strcmpi(B,'.xlsx')
+0038     EM='As of RAVEN version 1.9, only export to xlsx format is supported';
+0039     dispEM(EM);
 0040 end
 0041 
-0042 %Load an empty workbook
-0043 wb=loadWorkbook(filename,true);
-0044 
-0045 %Construct equations
-0046 model.equations=constructEquations(model,model.rxns,true);
-0047 
-0048 %Check if it should print genes
-0049 if isfield(model,'grRules')
-0050     rules=model.grRules;
-0051 else
-0052     rules=[];
-0053 end
-0054 
-0055 %Check if the model has default upper/lower bounds. This determines if
-0056 %those values should be printed or not
-0057 hasDefaultLB=false;
-0058 hasDefaultUB=false;
-0059 if isfield(model,'annotation')
-0060     if isfield(model.annotation,'defaultLB')
-0061         hasDefaultLB=true;
-0062     end
-0063     if isfield(model.annotation,'defaultUB')
-0064         hasDefaultUB=true;
-0065     end
-0066 end
-0067 
-0068 %Add the RXNS sheet
-0069 
-0070 %Create the header row
-0071 headers={'#';'ID';'NAME';'EQUATION';'EC-NUMBER';'GENE ASSOCIATION';'LOWER BOUND';'UPPER BOUND';'OBJECTIVE';'COMPARTMENT';'MIRIAM';'SUBSYSTEM';'REPLACEMENT ID';'NOTE';'REFERENCE';'CONFIDENCE SCORE'};
-0072 
-0073 %Add empty comments
-0074 emptyColumn=cell(numel(model.rxns),1);
-0075 rxnSheet=emptyColumn;
+0042 import java.io.File;
+0043 import java.io.FileOutputStream;
+0044 import java.io.IOException;
+0045 
+0046 %Remove the output file if it already exists
+0047 if exist(filename,'file')
+0048     delete(filename);
+0049 end
+0050 
+0051 %Load an empty workbook
+0052 wb=loadWorkbook(filename,true);
+0053 
+0054 %Construct equations
+0055 model.equations=constructEquations(model,model.rxns,true);
+0056 
+0057 %Check if it should print genes
+0058 if isfield(model,'grRules')
+0059     rules=model.grRules;
+0060 else
+0061     rules=[];
+0062 end
+0063 
+0064 %Check if the model has default upper/lower bounds. This determines if
+0065 %those values should be printed or not
+0066 hasDefaultLB=false;
+0067 hasDefaultUB=false;
+0068 if isfield(model,'annotation')
+0069     if isfield(model.annotation,'defaultLB')
+0070         hasDefaultLB=true;
+0071     end
+0072     if isfield(model.annotation,'defaultUB')
+0073         hasDefaultUB=true;
+0074     end
+0075 end
 0076 
-0077 %Add the model fields
-0078 rxnSheet=[rxnSheet model.rxns];
-0079 
-0080 if isfield(model,'rxnNames')
-0081     rxnSheet=[rxnSheet model.rxnNames];
-0082 else
-0083     rxnSheet=[rxnSheet emptyColumn];
-0084 end
+0077 %Add the RXNS sheet
+0078 
+0079 %Create the header row
+0080 headers={'#';'ID';'NAME';'EQUATION';'EC-NUMBER';'GENE ASSOCIATION';'LOWER BOUND';'UPPER BOUND';'OBJECTIVE';'COMPARTMENT';'MIRIAM';'SUBSYSTEM';'REPLACEMENT ID';'NOTE';'REFERENCE';'CONFIDENCE SCORE'};
+0081 
+0082 %Add empty comments
+0083 emptyColumn=cell(numel(model.rxns),1);
+0084 rxnSheet=emptyColumn;
 0085 
-0086 rxnSheet=[rxnSheet model.equations];
-0087 
-0088 if isfield(model,'eccodes')
-0089     rxnSheet=[rxnSheet model.eccodes];
-0090 else
-0091     rxnSheet=[rxnSheet emptyColumn];
-0092 end
-0093 
-0094 if ~isempty(rules)
-0095     rxnSheet=[rxnSheet rules];
-0096 else
-0097     rxnSheet=[rxnSheet emptyColumn];
-0098 end
-0099 
-0100 lb=emptyColumn;
-0101 ub=emptyColumn;
-0102 objective=emptyColumn;
-0103 rxnMiriams=emptyColumn;
-0104 
-0105 for i=1:numel(model.rxns)
-0106     if isfield(model,'lb')
-0107         if hasDefaultLB==true
-0108             if model.rev(i)==1
-0109                 %If reversible, print only if different than defaultLB
-0110                 if model.lb(i) ~= model.annotation.defaultLB
-0111                     lb{i}=model.lb(i);
-0112                 end
-0113             else
-0114                 %If irreversible, print only for non-zero values
-0115                 if model.lb(i)~=0
-0116                     lb{i}=model.lb(i);
-0117                 end
-0118             end
-0119         else
-0120             lb{i}=model.lb(i);
-0121         end
-0122     end
-0123     
-0124     if isfield(model,'ub')
-0125         if hasDefaultUB==true
-0126             if model.ub(i) ~= model.annotation.defaultUB
-0127                 ub{i}=model.ub(i);
-0128             end
-0129         else
-0130             ub{i}=model.ub(i);
-0131         end
-0132     end
-0133     
-0134     if isfield(model,'c')
-0135         if model.c(i)~=0
-0136             objective{i}=model.c(i);
-0137         end
-0138     end
-0139     
-0140     if isfield(model,'rxnMiriams')
-0141         if ~isempty(model.rxnMiriams{i})
-0142             toPrint=[];
-0143             for j=1:numel(model.rxnMiriams{i}.name)
-0144                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
-0145             end
-0146             rxnMiriams{i}=toPrint(1:end-1);
-0147         end
-0148     end
-0149 end
-0150 
-0151 rxnSheet=[rxnSheet lb];
-0152 rxnSheet=[rxnSheet ub];
-0153 rxnSheet=[rxnSheet objective];
-0154 
-0155 if isfield(model,'rxnComps')
-0156     rxnSheet=[rxnSheet model.comps(model.rxnComps)];
-0157 else
-0158     rxnSheet=[rxnSheet emptyColumn];
-0159 end
-0160 
-0161 rxnSheet=[rxnSheet rxnMiriams];
-0162 
-0163 subsystems='';
-0164 if isfield(model,'subSystems')
-0165     for i=1:numel(model.subSystems)
-0166         if ~isempty(model.subSystems{i,1})
-0167             subsystems{i,1}=strjoin(model.subSystems{i,1},';');
-0168         else
-0169             subsystems{i,1}='';
-0170         end
-0171     end
-0172     rxnSheet=[rxnSheet subsystems];
-0173 else
-0174     rxnSheet=[rxnSheet emptyColumn];
-0175 end
-0176 
-0177 %For REPLACEMENT ID which isn't in the model
-0178 rxnSheet=[rxnSheet emptyColumn];
-0179 
-0180 if isfield(model,'rxnNotes')
-0181     rxnSheet=[rxnSheet model.rxnNotes];
+0086 %Add the model fields
+0087 rxnSheet=[rxnSheet model.rxns];
+0088 
+0089 if isfield(model,'rxnNames')
+0090     rxnSheet=[rxnSheet model.rxnNames];
+0091 else
+0092     rxnSheet=[rxnSheet emptyColumn];
+0093 end
+0094 
+0095 rxnSheet=[rxnSheet model.equations];
+0096 
+0097 if isfield(model,'eccodes')
+0098     rxnSheet=[rxnSheet model.eccodes];
+0099 else
+0100     rxnSheet=[rxnSheet emptyColumn];
+0101 end
+0102 
+0103 if ~isempty(rules)
+0104     rxnSheet=[rxnSheet rules];
+0105 else
+0106     rxnSheet=[rxnSheet emptyColumn];
+0107 end
+0108 
+0109 lb=emptyColumn;
+0110 ub=emptyColumn;
+0111 objective=emptyColumn;
+0112 rxnMiriams=emptyColumn;
+0113 
+0114 for i=1:numel(model.rxns)
+0115     if isfield(model,'lb')
+0116         if hasDefaultLB==true
+0117             if model.rev(i)==1
+0118                 %If reversible, print only if different than defaultLB
+0119                 if model.lb(i) ~= model.annotation.defaultLB
+0120                     lb{i}=model.lb(i);
+0121                 end
+0122             else
+0123                 %If irreversible, print only for non-zero values
+0124                 if model.lb(i)~=0
+0125                     lb{i}=model.lb(i);
+0126                 end
+0127             end
+0128         else
+0129             lb{i}=model.lb(i);
+0130         end
+0131     end
+0132     
+0133     if isfield(model,'ub')
+0134         if hasDefaultUB==true
+0135             if model.ub(i) ~= model.annotation.defaultUB
+0136                 ub{i}=model.ub(i);
+0137             end
+0138         else
+0139             ub{i}=model.ub(i);
+0140         end
+0141     end
+0142     
+0143     if isfield(model,'c')
+0144         if model.c(i)~=0
+0145             objective{i}=model.c(i);
+0146         end
+0147     end
+0148     
+0149     if isfield(model,'rxnMiriams')
+0150         if ~isempty(model.rxnMiriams{i})
+0151             toPrint=[];
+0152             for j=1:numel(model.rxnMiriams{i}.name)
+0153                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
+0154             end
+0155             rxnMiriams{i}=toPrint(1:end-1);
+0156         end
+0157     end
+0158 end
+0159 
+0160 rxnSheet=[rxnSheet lb];
+0161 rxnSheet=[rxnSheet ub];
+0162 rxnSheet=[rxnSheet objective];
+0163 
+0164 if isfield(model,'rxnComps')
+0165     rxnSheet=[rxnSheet model.comps(model.rxnComps)];
+0166 else
+0167     rxnSheet=[rxnSheet emptyColumn];
+0168 end
+0169 
+0170 rxnSheet=[rxnSheet rxnMiriams];
+0171 
+0172 subsystems='';
+0173 if isfield(model,'subSystems')
+0174     for i=1:numel(model.subSystems)
+0175         if ~isempty(model.subSystems{i,1})
+0176             subsystems{i,1}=strjoin(model.subSystems{i,1},';');
+0177         else
+0178             subsystems{i,1}='';
+0179         end
+0180     end
+0181     rxnSheet=[rxnSheet subsystems];
 0182 else
 0183     rxnSheet=[rxnSheet emptyColumn];
 0184 end
 0185 
-0186 if isfield(model,'rxnReferences')
-0187     rxnSheet=[rxnSheet model.rxnReferences];
-0188 else
-0189     rxnSheet=[rxnSheet emptyColumn];
-0190 end
-0191 
-0192 if isfield(model,'rxnConfidenceScores')
-0193     rxnSheet=[rxnSheet num2cell(model.rxnConfidenceScores)];
-0194 else
-0195     rxnSheet=[rxnSheet emptyColumn];
-0196 end
-0197 
-0198 wb=writeSheet(wb,'RXNS',0,headers,[],rxnSheet);
-0199 
-0200 headers={'#';'ID';'NAME';'UNCONSTRAINED';'MIRIAM';'COMPOSITION';'InChI';'COMPARTMENT';'REPLACEMENT ID';'CHARGE'};
-0201 
-0202 metSheet=cell(numel(model.mets),numel(headers));
-0203 
-0204 for i=1:numel(model.mets)
-0205     metSheet{i,2}=[model.metNames{i} '[' model.comps{model.metComps(i)} ']'];
-0206     
-0207     if isfield(model,'metNames')
-0208         metSheet(i,3)=model.metNames(i);
-0209     end
-0210     
-0211     if isfield(model,'unconstrained')
-0212         if model.unconstrained(i)~=0
-0213             metSheet{i,4}=true;
-0214         end
-0215     end
-0216     
-0217     if isfield(model,'metMiriams')
-0218         if ~isempty(model.metMiriams{i})
-0219             toPrint=[];
-0220             for j=1:numel(model.metMiriams{i}.name)
-0221                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
-0222             end
-0223             metSheet{i,5}=toPrint(1:end-1);
-0224         end
-0225     end
-0226     
-0227     % Making sure that only these metFormulas are exported, which don't
-0228     % have InChI strings
-0229     if isfield(model,'metFormulas')
-0230         if isfield(model,'inchis')
-0231             if isempty(model.inchis{i})
-0232                 metSheet(i,6)=model.metFormulas(i);
-0233             end
-0234         else
-0235             metSheet(i,6)=model.metFormulas(i);
-0236         end
-0237     end
-0238     
-0239     if isfield(model,'inchis')
-0240         metSheet(i,7)=model.inchis(i);
-0241     end
-0242     
-0243     if isfield(model,'metComps')
-0244         metSheet(i,8)=model.comps(model.metComps(i));
-0245     end
-0246     
-0247     metSheet(i,9)=model.mets(i);
-0248     
-0249     if isfield(model,'metCharges')
-0250         metSheet{i,10}=model.metCharges(i);
-0251     end
-0252 end
-0253 
-0254 wb=writeSheet(wb,'METS',1,headers,[],metSheet);
-0255 
-0256 %Add the COMPS sheet
-0257 
-0258 %Create the header row
-0259 headers={'#';'ABBREVIATION';'NAME';'INSIDE';'MIRIAM'};
-0260 
-0261 compSheet=cell(numel(model.comps),numel(headers));
+0186 %For REPLACEMENT ID which isn't in the model
+0187 rxnSheet=[rxnSheet emptyColumn];
+0188 
+0189 if isfield(model,'rxnNotes')
+0190     rxnSheet=[rxnSheet model.rxnNotes];
+0191 else
+0192     rxnSheet=[rxnSheet emptyColumn];
+0193 end
+0194 
+0195 if isfield(model,'rxnReferences')
+0196     rxnSheet=[rxnSheet model.rxnReferences];
+0197 else
+0198     rxnSheet=[rxnSheet emptyColumn];
+0199 end
+0200 
+0201 if isfield(model,'rxnConfidenceScores')
+0202     rxnSheet=[rxnSheet num2cell(model.rxnConfidenceScores)];
+0203 else
+0204     rxnSheet=[rxnSheet emptyColumn];
+0205 end
+0206 
+0207 wb=writeSheet(wb,'RXNS',0,headers,[],rxnSheet);
+0208 
+0209 headers={'#';'ID';'NAME';'UNCONSTRAINED';'MIRIAM';'COMPOSITION';'InChI';'COMPARTMENT';'REPLACEMENT ID';'CHARGE'};
+0210 
+0211 metSheet=cell(numel(model.mets),numel(headers));
+0212 
+0213 for i=1:numel(model.mets)
+0214     metSheet{i,2}=[model.metNames{i} '[' model.comps{model.metComps(i)} ']'];
+0215     
+0216     if isfield(model,'metNames')
+0217         metSheet(i,3)=model.metNames(i);
+0218     end
+0219     
+0220     if isfield(model,'unconstrained')
+0221         if model.unconstrained(i)~=0
+0222             metSheet{i,4}=true;
+0223         end
+0224     end
+0225     
+0226     if isfield(model,'metMiriams')
+0227         if ~isempty(model.metMiriams{i})
+0228             toPrint=[];
+0229             for j=1:numel(model.metMiriams{i}.name)
+0230                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
+0231             end
+0232             metSheet{i,5}=toPrint(1:end-1);
+0233         end
+0234     end
+0235     
+0236     % Making sure that only these metFormulas are exported, which don't
+0237     % have InChI strings
+0238     if isfield(model,'metFormulas')
+0239         if isfield(model,'inchis')
+0240             if isempty(model.inchis{i})
+0241                 metSheet(i,6)=model.metFormulas(i);
+0242             end
+0243         else
+0244             metSheet(i,6)=model.metFormulas(i);
+0245         end
+0246     end
+0247     
+0248     if isfield(model,'inchis')
+0249         metSheet(i,7)=model.inchis(i);
+0250     end
+0251     
+0252     if isfield(model,'metComps')
+0253         metSheet(i,8)=model.comps(model.metComps(i));
+0254     end
+0255     
+0256     metSheet(i,9)=model.mets(i);
+0257     
+0258     if isfield(model,'metCharges')
+0259         metSheet{i,10}=model.metCharges(i);
+0260     end
+0261 end
 0262 
-0263 for i=1:numel(model.comps)
-0264     compSheet(i,2)=model.comps(i);
-0265     
-0266     if isfield(model,'compNames')
-0267         compSheet(i,3)=model.compNames(i);
-0268     end
-0269     
-0270     if isfield(model,'compOutside')
-0271         compSheet(i,4)=model.compOutside(i);
-0272     end
-0273     
-0274     if isfield(model,'compMiriams')
-0275         if ~isempty(model.compMiriams{i})
-0276             toPrint=[];
-0277             for j=1:numel(model.compMiriams{i}.name)
-0278                 toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
-0279             end
-0280             compSheet{i,5}=toPrint(1:end-1);
-0281         end
-0282     end
-0283 end
-0284 
-0285 wb=writeSheet(wb,'COMPS',2,headers,[],compSheet);
-0286 
-0287 %Add the GENES sheet
-0288 if isfield(model,'genes')
-0289     %Create the header row
-0290     headers={'#';'NAME';'MIRIAM';'SHORT NAME';'COMPARTMENT'};
-0291     
-0292     geneSheet=cell(numel(model.genes),numel(headers));
-0293     
-0294     for i=1:numel(model.genes)
-0295         geneSheet(i,2)=model.genes(i);
-0296         
-0297         if isfield(model,'geneMiriams')
-0298             if ~isempty(model.geneMiriams{i})
-0299                 toPrint=[];
-0300                 for j=1:numel(model.geneMiriams{i}.name)
-0301                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
-0302                 end
-0303                 geneSheet{i,3}=toPrint(1:end-1);
-0304             end
-0305         end
-0306         if isfield(model,'geneShortNames')
-0307             geneSheet(i,4)=model.geneShortNames(i);
-0308         end
-0309         if isfield(model,'geneComps')
-0310             geneSheet(i,5)=model.comps(model.geneComps(i));
-0311         end
-0312     end
-0313     
-0314     wb=writeSheet(wb,'GENES',3,headers,[],geneSheet);
-0315 end
-0316 
-0317 %Add the MODEL sheet
-0318 
-0319 %Create the header row
-0320 headers={'#';'ID';'NAME';'TAXONOMY';'DEFAULT LOWER';'DEFAULT UPPER';'CONTACT GIVEN NAME';'CONTACT FAMILY NAME';'CONTACT EMAIL';'ORGANIZATION';'NOTES'};
-0321 
-0322 modelSheet=cell(1,numel(headers));
-0323 
-0324 if ~isfield(model,'annotation')
-0325     model.annotation = [];
-0326 end
+0263 wb=writeSheet(wb,'METS',1,headers,[],metSheet);
+0264 
+0265 %Add the COMPS sheet
+0266 
+0267 %Create the header row
+0268 headers={'#';'ABBREVIATION';'NAME';'INSIDE';'MIRIAM'};
+0269 
+0270 compSheet=cell(numel(model.comps),numel(headers));
+0271 
+0272 for i=1:numel(model.comps)
+0273     compSheet(i,2)=model.comps(i);
+0274     
+0275     if isfield(model,'compNames')
+0276         compSheet(i,3)=model.compNames(i);
+0277     end
+0278     
+0279     if isfield(model,'compOutside')
+0280         compSheet(i,4)=model.compOutside(i);
+0281     end
+0282     
+0283     if isfield(model,'compMiriams')
+0284         if ~isempty(model.compMiriams{i})
+0285             toPrint=[];
+0286             for j=1:numel(model.compMiriams{i}.name)
+0287                 toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
+0288             end
+0289             compSheet{i,5}=toPrint(1:end-1);
+0290         end
+0291     end
+0292 end
+0293 
+0294 wb=writeSheet(wb,'COMPS',2,headers,[],compSheet);
+0295 
+0296 %Add the GENES sheet
+0297 if isfield(model,'genes')
+0298     %Create the header row
+0299     headers={'#';'NAME';'MIRIAM';'SHORT NAME';'COMPARTMENT'};
+0300     
+0301     geneSheet=cell(numel(model.genes),numel(headers));
+0302     
+0303     for i=1:numel(model.genes)
+0304         geneSheet(i,2)=model.genes(i);
+0305         
+0306         if isfield(model,'geneMiriams')
+0307             if ~isempty(model.geneMiriams{i})
+0308                 toPrint=[];
+0309                 for j=1:numel(model.geneMiriams{i}.name)
+0310                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
+0311                 end
+0312                 geneSheet{i,3}=toPrint(1:end-1);
+0313             end
+0314         end
+0315         if isfield(model,'geneShortNames')
+0316             geneSheet(i,4)=model.geneShortNames(i);
+0317         end
+0318         if isfield(model,'geneComps')
+0319             geneSheet(i,5)=model.comps(model.geneComps(i));
+0320         end
+0321     end
+0322     
+0323     wb=writeSheet(wb,'GENES',3,headers,[],geneSheet);
+0324 end
+0325 
+0326 %Add the MODEL sheet
 0327 
-0328 if isfield(model,'id')
-0329     modelSheet{1,2}=model.id;
-0330 else
-0331     modelSheet{1,2}='blankID';
-0332 end
-0333 if isfield(model,'name')
-0334     modelSheet{1,3}=model.name;
-0335 else
-0336     modelSheet{1,3}='blankName';
-0337 end
-0338 if isfield(model.annotation,'taxonomy')
-0339     modelSheet{1,4}=model.annotation.taxonomy;
-0340 end
-0341 if isfield(model.annotation,'defaultLB')
-0342     modelSheet{1,5}=model.annotation.defaultLB;
-0343 end
-0344 if isfield(model.annotation,'defaultUB')
-0345     modelSheet{1,6}=model.annotation.defaultUB;
+0328 %Create the header row
+0329 headers={'#';'ID';'NAME';'TAXONOMY';'DEFAULT LOWER';'DEFAULT UPPER';'CONTACT GIVEN NAME';'CONTACT FAMILY NAME';'CONTACT EMAIL';'ORGANIZATION';'NOTES'};
+0330 
+0331 modelSheet=cell(1,numel(headers));
+0332 
+0333 if ~isfield(model,'annotation')
+0334     model.annotation = [];
+0335 end
+0336 
+0337 if isfield(model,'id')
+0338     modelSheet{1,2}=model.id;
+0339 else
+0340     modelSheet{1,2}='blankID';
+0341 end
+0342 if isfield(model,'name')
+0343     modelSheet{1,3}=model.name;
+0344 else
+0345     modelSheet{1,3}='blankName';
 0346 end
-0347 if isfield(model.annotation,'givenName')
-0348     modelSheet{1,7}=model.annotation.givenName;
+0347 if isfield(model.annotation,'taxonomy')
+0348     modelSheet{1,4}=model.annotation.taxonomy;
 0349 end
-0350 if isfield(model.annotation,'familyName')
-0351     modelSheet{1,8}=model.annotation.familyName;
+0350 if isfield(model.annotation,'defaultLB')
+0351     modelSheet{1,5}=model.annotation.defaultLB;
 0352 end
-0353 if isfield(model.annotation,'email')
-0354     modelSheet{1,9}=model.annotation.email;
+0353 if isfield(model.annotation,'defaultUB')
+0354     modelSheet{1,6}=model.annotation.defaultUB;
 0355 end
-0356 if isfield(model.annotation,'organization')
-0357     modelSheet{1,10}=model.annotation.organization;
+0356 if isfield(model.annotation,'givenName')
+0357     modelSheet{1,7}=model.annotation.givenName;
 0358 end
-0359 if isfield(model.annotation,'note')
-0360     modelSheet{1,11}=model.annotation.note;
+0359 if isfield(model.annotation,'familyName')
+0360     modelSheet{1,8}=model.annotation.familyName;
 0361 end
-0362 
-0363 if isfield(model,'genes')
-0364     wb=writeSheet(wb,'MODEL',4,headers,[],modelSheet);
-0365 else
-0366     wb=writeSheet(wb,'MODEL',3,headers,[],modelSheet);
+0362 if isfield(model.annotation,'email')
+0363     modelSheet{1,9}=model.annotation.email;
+0364 end
+0365 if isfield(model.annotation,'organization')
+0366     modelSheet{1,10}=model.annotation.organization;
 0367 end
-0368 
-0369 %Open the output stream
-0370 out = FileOutputStream(filename);
-0371 wb.write(out);
-0372 out.close();
-0373 end
    
+0368 if isfield(model.annotation,'note')
+0369     modelSheet{1,11}=model.annotation.note;
+0370 end
+0371 
+0372 if isfield(model,'genes')
+0373     wb=writeSheet(wb,'MODEL',4,headers,[],modelSheet);
+0374 else
+0375     wb=writeSheet(wb,'MODEL',3,headers,[],modelSheet);
+0376 end
+0377 
+0378 %Open the output stream
+0379 out = FileOutputStream(filename);
+0380 wb.write(out);
+0381 out.close();
+0382 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/exportToTabDelimited.html b/doc/io/exportToTabDelimited.html
index b35d6ca0..d570724b 100644
--- a/doc/io/exportToTabDelimited.html
+++ b/doc/io/exportToTabDelimited.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^exportToTabDelimited

    SYNOPSIS ^

    -
    function exportToTabDelimited(model,path)
    +
    function exportToTabDelimited(model,path,sortIds)

    DESCRIPTION ^

     exportToTabDelimited
@@ -34,6 +34,8 @@ 
    DESCRIPTION ^DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
    • 
 
 
 
 
 
    SOURCE CODE ^
    
-
    0001 function exportToTabDelimited(model,path)
+
    0001 function exportToTabDelimited(model,path,sortIds)
 0002 % exportToTabDelimited
 0003 %   Exports a model structure to a set of tab-delimited text files
 0004 %
@@ -65,330 +67,338 @@ 
    SOURCE CODE ^%   path    the path to export to. The resulting text files will be saved
 0007 %           under the names excelRxns.txt, excelMets.txt, excelGenes.txt,
 0008 %           excelModel.txt, and excelComps.txt
-0009 %
-0010 %   NOTE: This functionality was previously a part of exportToExcelFormat.
-0011 %         The naming of the resulting text files is to preserve backward
-0012 %         compatibility
-0013 %
-0014 %   NOTE: No checks are made regarding the correctness of the model. Use
-0015 %         checkModelStruct to identify problems in the model structure
-0016 %
-0017 %   Usage: exportToTabDelimited(model,path)
-0018 
-0019 if nargin<2
-0020     path='./';
-0021 end
-0022 
-0023 %If the folder doesn't exist then create it
-0024 if ~exist(path,'dir')
-0025     mkdir(path);
+0009 %   sortIds logical whether metabolites, reactions and genes should be
+0010 %           sorted alphabetically by their identifiers (opt, default false)
+0011 %
+0012 %   NOTE: This functionality was previously a part of exportToExcelFormat.
+0013 %         The naming of the resulting text files is to preserve backward
+0014 %         compatibility
+0015 %
+0016 %   NOTE: No checks are made regarding the correctness of the model. Use
+0017 %         checkModelStruct to identify problems in the model structure
+0018 %
+0019 %   Usage: exportToTabDelimited(model,path,sortIds)
+0020 
+0021 if nargin<2
+0022     path='./';
+0023 end
+0024 if nargin<3
+0025     sortIds=false;
 0026 end
-0027 
-0028 %Remove the files if they already exist
-0029 if exist(fullfile(path,'excelRxns.txt'),'file')
-0030     delete(fullfile(path,'excelRxns.txt'));
-0031 end
-0032 if exist(fullfile(path,'excelMets.txt'),'file')
-0033     delete(fullfile(path,'excelMets.txt'));
+0027 if sortIds==true
+0028     model=sortIdentifiers(model);
+0029 end
+0030 
+0031 %If the folder doesn't exist then create it
+0032 if ~exist(path,'dir')
+0033     mkdir(path);
 0034 end
-0035 if exist(fullfile(path,'excelGenes.txt'),'file')
-0036     delete(fullfile(path,'excelGenes.txt'));
-0037 end
-0038 if exist(fullfile(path,'excelModel.txt'),'file')
-0039     delete(fullfile(path,'excelModel.txt'));
-0040 end
-0041 if exist(fullfile(path,'excelComps.txt'),'file')
-0042     delete(fullfile(path,'excelComps.txt'));
-0043 end
-0044 
-0045 %Construct equations
-0046 model.equations=constructEquations(model,model.rxns,true);
-0047 
-0048 %Open for printing the rxn sheet
-0049 rxnFile=fopen(fullfile(path,'excelRxns.txt'),'wt');
-0050 
-0051 %Print header
-0052 fprintf(rxnFile,'#\tID\tNAME\tEQUATION\tEC-NUMBER\tGENE ASSOCIATION\tLOWER BOUND\tUPPER BOUND\tOBJECTIVE\tCOMPARTMENT\tMIRIAM\tSUBSYSTEM\tREPLACEMENT ID\tNOTE\tREFERENCE\tCONFIDENCE SCORE\n');
-0053 
-0054 %Loop through the reactions
-0055 for i=1:numel(model.rxns)
-0056     fprintf(rxnFile,['\t' model.rxns{i} '\t' model.rxnNames{i} '\t' model.equations{i} '\t']);
-0057     
-0058     if isfield(model,'eccodes')
-0059         fprintf(rxnFile,[model.eccodes{i} '\t']);
-0060     else
-0061         fprintf(rxnFile,'\t');
-0062     end
-0063     
-0064     if isfield(model,'grRules')
-0065         fprintf(rxnFile,[model.grRules{i} '\t']);
-0066     else
-0067         fprintf(rxnFile,'\t');
-0068     end
-0069     
-0070     %Print bounds and objectives
-0071     fprintf(rxnFile,[num2str(model.lb(i)) '\t' num2str(model.ub(i)) '\t']);
-0072     
-0073     if model.c(i)~=0
-0074         fprintf(rxnFile,[num2str(model.c(i)) '\t' ]);
-0075     else
-0076         fprintf(rxnFile,'\t');
-0077     end
-0078     
-0079     if isfield(model,'rxnComps')
-0080         fprintf(rxnFile,[model.comps{model.rxnComps(i)} '\t']);
-0081     else
-0082         fprintf(rxnFile,'\t');
-0083     end
-0084     
-0085     if isfield(model,'rxnMiriams')
-0086         if ~isempty(model.rxnMiriams{i})
-0087             toPrint=[];
-0088             for j=1:numel(model.rxnMiriams{i}.name)
-0089                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
-0090             end
-0091             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
-0092         else
-0093             fprintf(rxnFile,'\t');
-0094         end
-0095     else
-0096         fprintf(rxnFile,'\t');
-0097     end
-0098     
-0099     if isfield(model,'subSystems')
-0100         if ~isempty(model.subSystems{i})
-0101             fprintf(rxnFile,[strjoin(model.subSystems{i,1},';') '\t']);
-0102         else
-0103             fprintf(rxnFile,'\t');
-0104         end
+0035 
+0036 %Remove the files if they already exist
+0037 if exist(fullfile(path,'excelRxns.txt'),'file')
+0038     delete(fullfile(path,'excelRxns.txt'));
+0039 end
+0040 if exist(fullfile(path,'excelMets.txt'),'file')
+0041     delete(fullfile(path,'excelMets.txt'));
+0042 end
+0043 if exist(fullfile(path,'excelGenes.txt'),'file')
+0044     delete(fullfile(path,'excelGenes.txt'));
+0045 end
+0046 if exist(fullfile(path,'excelModel.txt'),'file')
+0047     delete(fullfile(path,'excelModel.txt'));
+0048 end
+0049 if exist(fullfile(path,'excelComps.txt'),'file')
+0050     delete(fullfile(path,'excelComps.txt'));
+0051 end
+0052 
+0053 %Construct equations
+0054 model.equations=constructEquations(model,model.rxns,true);
+0055 
+0056 %Open for printing the rxn sheet
+0057 rxnFile=fopen(fullfile(path,'excelRxns.txt'),'wt');
+0058 
+0059 %Print header
+0060 fprintf(rxnFile,'#\tID\tNAME\tEQUATION\tEC-NUMBER\tGENE ASSOCIATION\tLOWER BOUND\tUPPER BOUND\tOBJECTIVE\tCOMPARTMENT\tMIRIAM\tSUBSYSTEM\tREPLACEMENT ID\tNOTE\tREFERENCE\tCONFIDENCE SCORE\n');
+0061 
+0062 %Loop through the reactions
+0063 for i=1:numel(model.rxns)
+0064     fprintf(rxnFile,['\t' model.rxns{i} '\t' model.rxnNames{i} '\t' model.equations{i} '\t']);
+0065     
+0066     if isfield(model,'eccodes')
+0067         fprintf(rxnFile,[model.eccodes{i} '\t']);
+0068     else
+0069         fprintf(rxnFile,'\t');
+0070     end
+0071     
+0072     if isfield(model,'grRules')
+0073         fprintf(rxnFile,[model.grRules{i} '\t']);
+0074     else
+0075         fprintf(rxnFile,'\t');
+0076     end
+0077     
+0078     %Print bounds and objectives
+0079     fprintf(rxnFile,[num2str(model.lb(i)) '\t' num2str(model.ub(i)) '\t']);
+0080     
+0081     if model.c(i)~=0
+0082         fprintf(rxnFile,[num2str(model.c(i)) '\t' ]);
+0083     else
+0084         fprintf(rxnFile,'\t');
+0085     end
+0086     
+0087     if isfield(model,'rxnComps')
+0088         fprintf(rxnFile,[model.comps{model.rxnComps(i)} '\t']);
+0089     else
+0090         fprintf(rxnFile,'\t');
+0091     end
+0092     
+0093     if isfield(model,'rxnMiriams')
+0094         if ~isempty(model.rxnMiriams{i})
+0095             toPrint=[];
+0096             for j=1:numel(model.rxnMiriams{i}.name)
+0097                 toPrint=[toPrint strtrim(model.rxnMiriams{i}.name{j}) '/' strtrim(model.rxnMiriams{i}.value{j}) ';'];
+0098             end
+0099             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
+0100         else
+0101             fprintf(rxnFile,'\t');
+0102         end
+0103     else
+0104         fprintf(rxnFile,'\t');
 0105     end
 0106     
-0107     %Print replacement IDs
-0108     fprintf(rxnFile,'\t');
-0109     
-0110     if isfield(model,'rxnNotes')
-0111         fprintf(rxnFile,[model.rxnNotes{i} '\t']);
-0112     else
-0113         fprintf(rxnFile,'\t');
-0114     end
-0115     
-0116     if isfield(model,'rxnReferences')
-0117         fprintf(rxnFile,[model.rxnReferences{i} '\t']);
-0118     else
-0119         fprintf(rxnFile,'\t');
-0120     end
-0121     
-0122     if isfield(model,'rxnConfidenceScores')
-0123         fprintf(rxnFile,[num2str(model.rxnConfidenceScores(i)) '\t' ]);
-0124     else
-0125         fprintf(rxnFile,'\t');
-0126     end
-0127     
-0128     fprintf(rxnFile,'\n');
-0129 end
-0130 
-0131 fclose(rxnFile);
-0132 
-0133 %Open for printing the metabolites sheet
-0134 metFile=fopen(fullfile(path,'excelMets.txt'),'wt');
-0135 
-0136 %Print header
-0137 fprintf(metFile,'#\tID\tNAME\tUNCONSTRAINED\tMIRIAM\tCOMPOSITION\tInChI\tCOMPARTMENT\tREPLACEMENT ID\tMETS FIELD\tCHARGE\n');
+0107     if isfield(model,'subSystems')
+0108         if ~isempty(model.subSystems{i})
+0109             fprintf(rxnFile,[strjoin(model.subSystems{i,1},';') '\t']);
+0110         else
+0111             fprintf(rxnFile,'\t');
+0112         end
+0113     end
+0114     
+0115     %Print replacement IDs
+0116     fprintf(rxnFile,'\t');
+0117     
+0118     if isfield(model,'rxnNotes')
+0119         fprintf(rxnFile,[model.rxnNotes{i} '\t']);
+0120     else
+0121         fprintf(rxnFile,'\t');
+0122     end
+0123     
+0124     if isfield(model,'rxnReferences')
+0125         fprintf(rxnFile,[model.rxnReferences{i} '\t']);
+0126     else
+0127         fprintf(rxnFile,'\t');
+0128     end
+0129     
+0130     if isfield(model,'rxnConfidenceScores')
+0131         fprintf(rxnFile,[num2str(model.rxnConfidenceScores(i)) '\t' ]);
+0132     else
+0133         fprintf(rxnFile,'\t');
+0134     end
+0135     
+0136     fprintf(rxnFile,'\n');
+0137 end
 0138 
-0139 %Loop through the metabolites
-0140 for i=1:numel(model.mets)
-0141     fprintf(metFile,['\t' model.metNames{i} '[' model.comps{model.metComps(i)} ']\t' model.metNames{i} '\t']);
-0142     
-0143     if isfield(model,'unconstrained')
-0144         if model.unconstrained(i)~=0
-0145             fprintf(metFile,'TRUE\t');
-0146         else
-0147             fprintf(metFile,'\t');
-0148         end
-0149     else
-0150         fprintf(metFile,'\t');
-0151     end
-0152     
-0153     if isfield(model,'metMiriams')
-0154         if ~isempty(model.metMiriams{i})
-0155             toPrint=[];
-0156             for j=1:numel(model.metMiriams{i}.name)
-0157                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
-0158             end
-0159             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
-0160         else
-0161             fprintf(metFile,'\t');
-0162         end
-0163     else
-0164         fprintf(metFile,'\t');
-0165     end
-0166     
-0167     if isfield(model,'metFormulas')
-0168         fprintf(metFile,[model.metFormulas{i} '\t']);
-0169     else
-0170         fprintf(metFile,'\t');
-0171     end
-0172     
-0173     if isfield(model,'inchis')
-0174         fprintf(metFile,[model.inchis{i} '\t']);
-0175     else
-0176         fprintf(metFile,'\t');
-0177     end
-0178     
-0179     fprintf(metFile,[model.comps{model.metComps(i)} '\t']);
+0139 fclose(rxnFile);
+0140 
+0141 %Open for printing the metabolites sheet
+0142 metFile=fopen(fullfile(path,'excelMets.txt'),'wt');
+0143 
+0144 %Print header
+0145 fprintf(metFile,'#\tID\tNAME\tUNCONSTRAINED\tMIRIAM\tCOMPOSITION\tInChI\tCOMPARTMENT\tREPLACEMENT ID\tMETS FIELD\tCHARGE\n');
+0146 
+0147 %Loop through the metabolites
+0148 for i=1:numel(model.mets)
+0149     fprintf(metFile,['\t' model.metNames{i} '[' model.comps{model.metComps(i)} ']\t' model.metNames{i} '\t']);
+0150     
+0151     if isfield(model,'unconstrained')
+0152         if model.unconstrained(i)~=0
+0153             fprintf(metFile,'TRUE\t');
+0154         else
+0155             fprintf(metFile,'\t');
+0156         end
+0157     else
+0158         fprintf(metFile,'\t');
+0159     end
+0160     
+0161     if isfield(model,'metMiriams')
+0162         if ~isempty(model.metMiriams{i})
+0163             toPrint=[];
+0164             for j=1:numel(model.metMiriams{i}.name)
+0165                 toPrint=[toPrint strtrim(model.metMiriams{i}.name{j}) '/' strtrim(model.metMiriams{i}.value{j}) ';'];
+0166             end
+0167             fprintf(rxnFile,[toPrint(1:end-1) '\t']);
+0168         else
+0169             fprintf(metFile,'\t');
+0170         end
+0171     else
+0172         fprintf(metFile,'\t');
+0173     end
+0174     
+0175     if isfield(model,'metFormulas')
+0176         fprintf(metFile,[model.metFormulas{i} '\t']);
+0177     else
+0178         fprintf(metFile,'\t');
+0179     end
 0180     
-0181     %There can be no replacement IDs in the structure, but it has to be
-0182     %something to give working met IDs.
-0183     fprintf(metFile,['m' int2str(i) '\t']);
-0184     
-0185     %Print the model.mets field. The reason for not putting this as
-0186     %replacement ID is that it's not guaranteed to be a valid SBML id.
-0187     fprintf(metFile,[model.mets{i} '\t']);
+0181     if isfield(model,'inchis')
+0182         fprintf(metFile,[model.inchis{i} '\t']);
+0183     else
+0184         fprintf(metFile,'\t');
+0185     end
+0186     
+0187     fprintf(metFile,[model.comps{model.metComps(i)} '\t']);
 0188     
-0189     if isfield(model,'metCharges')
-0190         fprintf(metFile,[num2str(model.metCharges(i)) '\t']);
-0191     else
-0192         fprintf(metFile,'\t');
-0193     end
-0194     
-0195     fprintf(metFile,'\n');
-0196 end
-0197 
-0198 fclose(metFile);
-0199 
-0200 if isfield(model,'genes')
-0201     %Open for printing the genes sheet
-0202     geneFile=fopen(fullfile(path,'excelGenes.txt'),'wt');
-0203     
-0204     %Print header
-0205     fprintf(geneFile,'#\tNAME\tMIRIAM\tSHORT NAME\tCOMPARTMENT\n');
-0206     
-0207     %Loop through the genes
-0208     for i=1:numel(model.genes)
-0209         fprintf(geneFile,['\t' model.genes{i} '\t']);
-0210         
-0211         if isfield(model,'geneMiriams')
-0212             if ~isempty(model.geneMiriams{i})
-0213                 toPrint=[];
-0214                 for j=1:numel(model.geneMiriams{i}.name)
-0215                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
-0216                 end
-0217                 fprintf(geneFile,[toPrint(1:end-1) '\t']);
-0218             else
-0219                 fprintf(geneFile,'\t');
-0220             end
-0221         else
-0222             fprintf(geneFile,'\t');
-0223         end
-0224         
-0225         if isfield(model,'geneShortNames')
-0226             fprintf(geneFile,[model.geneShortNames{i} '\t']);
-0227         else
-0228             fprintf(geneFile,'\t');
-0229         end
-0230         
-0231         if isfield(model,'geneComps')
-0232             fprintf(geneFile,[model.comps{model.geneComps(i)} '\t']);
-0233         else
-0234             fprintf(geneFile,'\t');
-0235         end
-0236         
-0237         fprintf(geneFile,'\n');
-0238     end
-0239     fclose(geneFile);
-0240 end
-0241 
-0242 if isfield(model,'id')
-0243     %Open for printing the model sheet
-0244     modelFile=fopen(fullfile(path,'excelModel.txt'),'wt');
-0245     
-0246     %Print header
-0247     fprintf(geneFile,'#\tID\tNAME\tDEFAULT LOWER\tDEFAULT UPPER\tCONTACT GIVEN NAME\tCONTACT FAMILY NAME\tCONTACT EMAIL\tORGANIZATION\tTAXONOMY\tNOTES\n');
-0248     
-0249     %Print model ID and name. It is assumed that the default lower/upper
-0250     %bound correspond to min/max of the bounds
-0251     toPrint=['\t' model.id '\t' model.name '\t'];
-0252     if isfield(model,'annotation')
-0253         if isfield(model.annotation,'defaultLB')
-0254             toPrint=[toPrint num2str(model.annotation.defaultLB) '\t'];
-0255         else
-0256             toPrint=[toPrint num2str(min(model.lb)) '\t'];
-0257         end
-0258         if isfield(model.annotation,'defaultUB')
-0259             toPrint=[toPrint num2str(model.annotation.defaultUB) '\t'];
-0260         else
-0261             toPrint=[toPrint num2str(max(model.ub)) '\t'];
-0262         end
-0263         if isfield(model.annotation,'givenName')
-0264             toPrint=[toPrint model.annotation.givenName '\t'];
-0265         else
-0266             toPrint=[toPrint '\t'];
-0267         end
-0268         if isfield(model.annotation,'familyName')
-0269             toPrint=[toPrint model.annotation.familyName '\t'];
-0270         else
-0271             toPrint=[toPrint '\t'];
-0272         end
-0273         if isfield(model.annotation,'email')
-0274             toPrint=[toPrint model.annotation.email '\t'];
-0275         else
-0276             toPrint=[toPrint '\t'];
-0277         end
-0278         if isfield(model.annotation,'organization')
-0279             toPrint=[toPrint model.annotation.organization '\t'];
-0280         else
-0281             toPrint=[toPrint '\t'];
-0282         end
-0283         if isfield(model.annotation,'taxonomy')
-0284             toPrint=[toPrint model.annotation.taxonomy '\t'];
-0285         else
-0286             toPrint=[toPrint '\t'];
-0287         end
-0288         if isfield(model.annotation,'note')
-0289             toPrint=[toPrint model.annotation.note '\t'];
-0290         else
-0291             toPrint=[toPrint '\t'];
-0292         end
-0293     else
-0294         toPrint=[toPrint num2str(min(model.lb)) '\t' num2str(max(model.ub)) '\t\t\t\t\t\t\n'];
-0295     end
-0296     fprintf(modelFile,toPrint);
-0297     fclose(modelFile);
-0298 end
-0299 
-0300 if isfield(model,'comps')
-0301     %Open for printing the model sheet
-0302     compsFile=fopen(fullfile(path,'excelComps.txt'),'wt');
-0303     
-0304     %Print header
-0305     fprintf(compsFile,'#\tABBREVIATION\tNAME\tINSIDE\tMIRIAM\n');
-0306     
-0307     for i=1:numel(model.comps)
-0308         toPrint=['\t' model.comps{i} '\t' model.compNames{i} '\t'];
-0309         if isfield(model,'compOutside')
-0310             toPrint=[toPrint model.compOutside{i} '\t'];
-0311         else
-0312             toPrint=[toPrint '\t'];
-0313         end
-0314         if isfield(model,'compMiriams')
-0315             if ~isempty(model.compMiriams{i})
-0316                 for j=1:numel(model.compMiriams{i}.name)
-0317                     toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
-0318                 end
-0319                 toPrint(end)=[];
-0320                 toPrint=[toPrint '\t'];
-0321             else
-0322                 toPrint=[toPrint '\t'];
-0323             end
-0324         else
-0325             toPrint=[toPrint '\t'];
-0326         end
-0327         toPrint=[toPrint '\n'];
-0328         fprintf(compsFile,toPrint);
-0329     end
-0330     fclose(compsFile);
-0331 end
-0332 end
    
+0189     %There can be no replacement IDs in the structure, but it has to be
+0190     %something to give working met IDs.
+0191     fprintf(metFile,['m' int2str(i) '\t']);
+0192     
+0193     %Print the model.mets field. The reason for not putting this as
+0194     %replacement ID is that it's not guaranteed to be a valid SBML id.
+0195     fprintf(metFile,[model.mets{i} '\t']);
+0196     
+0197     if isfield(model,'metCharges')
+0198         fprintf(metFile,[num2str(model.metCharges(i)) '\t']);
+0199     else
+0200         fprintf(metFile,'\t');
+0201     end
+0202     
+0203     fprintf(metFile,'\n');
+0204 end
+0205 
+0206 fclose(metFile);
+0207 
+0208 if isfield(model,'genes')
+0209     %Open for printing the genes sheet
+0210     geneFile=fopen(fullfile(path,'excelGenes.txt'),'wt');
+0211     
+0212     %Print header
+0213     fprintf(geneFile,'#\tNAME\tMIRIAM\tSHORT NAME\tCOMPARTMENT\n');
+0214     
+0215     %Loop through the genes
+0216     for i=1:numel(model.genes)
+0217         fprintf(geneFile,['\t' model.genes{i} '\t']);
+0218         
+0219         if isfield(model,'geneMiriams')
+0220             if ~isempty(model.geneMiriams{i})
+0221                 toPrint=[];
+0222                 for j=1:numel(model.geneMiriams{i}.name)
+0223                     toPrint=[toPrint strtrim(model.geneMiriams{i}.name{j}) '/' strtrim(model.geneMiriams{i}.value{j}) ';'];
+0224                 end
+0225                 fprintf(geneFile,[toPrint(1:end-1) '\t']);
+0226             else
+0227                 fprintf(geneFile,'\t');
+0228             end
+0229         else
+0230             fprintf(geneFile,'\t');
+0231         end
+0232         
+0233         if isfield(model,'geneShortNames')
+0234             fprintf(geneFile,[model.geneShortNames{i} '\t']);
+0235         else
+0236             fprintf(geneFile,'\t');
+0237         end
+0238         
+0239         if isfield(model,'geneComps')
+0240             fprintf(geneFile,[model.comps{model.geneComps(i)} '\t']);
+0241         else
+0242             fprintf(geneFile,'\t');
+0243         end
+0244         
+0245         fprintf(geneFile,'\n');
+0246     end
+0247     fclose(geneFile);
+0248 end
+0249 
+0250 if isfield(model,'id')
+0251     %Open for printing the model sheet
+0252     modelFile=fopen(fullfile(path,'excelModel.txt'),'wt');
+0253     
+0254     %Print header
+0255     fprintf(geneFile,'#\tID\tNAME\tDEFAULT LOWER\tDEFAULT UPPER\tCONTACT GIVEN NAME\tCONTACT FAMILY NAME\tCONTACT EMAIL\tORGANIZATION\tTAXONOMY\tNOTES\n');
+0256     
+0257     %Print model ID and name. It is assumed that the default lower/upper
+0258     %bound correspond to min/max of the bounds
+0259     toPrint=['\t' model.id '\t' model.name '\t'];
+0260     if isfield(model,'annotation')
+0261         if isfield(model.annotation,'defaultLB')
+0262             toPrint=[toPrint num2str(model.annotation.defaultLB) '\t'];
+0263         else
+0264             toPrint=[toPrint num2str(min(model.lb)) '\t'];
+0265         end
+0266         if isfield(model.annotation,'defaultUB')
+0267             toPrint=[toPrint num2str(model.annotation.defaultUB) '\t'];
+0268         else
+0269             toPrint=[toPrint num2str(max(model.ub)) '\t'];
+0270         end
+0271         if isfield(model.annotation,'givenName')
+0272             toPrint=[toPrint model.annotation.givenName '\t'];
+0273         else
+0274             toPrint=[toPrint '\t'];
+0275         end
+0276         if isfield(model.annotation,'familyName')
+0277             toPrint=[toPrint model.annotation.familyName '\t'];
+0278         else
+0279             toPrint=[toPrint '\t'];
+0280         end
+0281         if isfield(model.annotation,'email')
+0282             toPrint=[toPrint model.annotation.email '\t'];
+0283         else
+0284             toPrint=[toPrint '\t'];
+0285         end
+0286         if isfield(model.annotation,'organization')
+0287             toPrint=[toPrint model.annotation.organization '\t'];
+0288         else
+0289             toPrint=[toPrint '\t'];
+0290         end
+0291         if isfield(model.annotation,'taxonomy')
+0292             toPrint=[toPrint model.annotation.taxonomy '\t'];
+0293         else
+0294             toPrint=[toPrint '\t'];
+0295         end
+0296         if isfield(model.annotation,'note')
+0297             toPrint=[toPrint model.annotation.note '\t'];
+0298         else
+0299             toPrint=[toPrint '\t'];
+0300         end
+0301     else
+0302         toPrint=[toPrint num2str(min(model.lb)) '\t' num2str(max(model.ub)) '\t\t\t\t\t\t\n'];
+0303     end
+0304     fprintf(modelFile,toPrint);
+0305     fclose(modelFile);
+0306 end
+0307 
+0308 if isfield(model,'comps')
+0309     %Open for printing the model sheet
+0310     compsFile=fopen(fullfile(path,'excelComps.txt'),'wt');
+0311     
+0312     %Print header
+0313     fprintf(compsFile,'#\tABBREVIATION\tNAME\tINSIDE\tMIRIAM\n');
+0314     
+0315     for i=1:numel(model.comps)
+0316         toPrint=['\t' model.comps{i} '\t' model.compNames{i} '\t'];
+0317         if isfield(model,'compOutside')
+0318             toPrint=[toPrint model.compOutside{i} '\t'];
+0319         else
+0320             toPrint=[toPrint '\t'];
+0321         end
+0322         if isfield(model,'compMiriams')
+0323             if ~isempty(model.compMiriams{i})
+0324                 for j=1:numel(model.compMiriams{i}.name)
+0325                     toPrint=[toPrint strtrim(model.compMiriams{i}.name{j}) '/' strtrim(model.compMiriams{i}.value{j}) ';'];
+0326                 end
+0327                 toPrint(end)=[];
+0328                 toPrint=[toPrint '\t'];
+0329             else
+0330                 toPrint=[toPrint '\t'];
+0331             end
+0332         else
+0333             toPrint=[toPrint '\t'];
+0334         end
+0335         toPrint=[toPrint '\n'];
+0336         fprintf(compsFile,toPrint);
+0337     end
+0338     fclose(compsFile);
+0339 end
+0340 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/io/getMD5Hash.html b/doc/io/getMD5Hash.html
new file mode 100644
index 00000000..6dbdb0ba
--- /dev/null
+++ b/doc/io/getMD5Hash.html
@@ -0,0 +1,117 @@
+
+
+
+  Description of getMD5Hash
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  io > getMD5Hash.m
    
+
+
+
+
    getMD5Hash
+
    
+
+
    PURPOSE ^
    
+
    getMD5Hash
    
+
+
    SYNOPSIS ^
    
+
    function md5Hash=getMD5Hash(inputFile,binEnd) 
    
+
+
    DESCRIPTION ^
    
+
     getMD5Hash
+   Calculates MD5 hash for a file
+
+   Input:
+   inputFile       string with the path to file for which MD5 hash should
+                   be calculated
+   binEnd          string that shows the operating system running in the
+                   client's computer. Use ".exe" for Windows, ".mac" for
+                   macOS or leave it blank for Linux (""). (opt, by
+                   default the function automatically detects the client's
+                   operating system)
+
+   Output:
+   md5Hash         string containing an MD5 hash for inputFile
+   
+   Usage: md5Hash=getMD5Hash(inputFile,binEnd)
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
+
+
    SOURCE CODE ^
    
+
    0001 function md5Hash=getMD5Hash(inputFile,binEnd)
+0002 % getMD5Hash
+0003 %   Calculates MD5 hash for a file
+0004 %
+0005 %   Input:
+0006 %   inputFile       string with the path to file for which MD5 hash should
+0007 %                   be calculated
+0008 %   binEnd          string that shows the operating system running in the
+0009 %                   client's computer. Use ".exe" for Windows, ".mac" for
+0010 %                   macOS or leave it blank for Linux (""). (opt, by
+0011 %                   default the function automatically detects the client's
+0012 %                   operating system)
+0013 %
+0014 %   Output:
+0015 %   md5Hash         string containing an MD5 hash for inputFile
+0016 %
+0017 %   Usage: md5Hash=getMD5Hash(inputFile,binEnd)
+0018 
+0019 if nargin<2
+0020     if isunix
+0021         if ismac
+0022             binEnd='.mac';
+0023         else
+0024             binEnd='';
+0025         end
+0026     elseif ispc
+0027         binEnd='.exe';
+0028     else
+0029         dispEM('Unknown OS, exiting.')
+0030         return
+0031     end
+0032 end
+0033 
+0034 %Check if binEnd is valid
+0035 if ~strcmp(binEnd,'.mac') && ~strcmp(binEnd,'') && ~strcmp(binEnd,'.exe')
+0036    dispEM('Unknown OS, exiting.')
+0037    return
+0038 end
+0039 
+0040 %Check file existence
+0041 inputFile=checkFileExistence(inputFile);
+0042 
+0043 %Get string containing an MD5 hash
+0044 switch binEnd
+0045     case '.mac'
+0046         [~, md5HashMessage]=system(['md5 "' inputFile '"']);
+0047     case ''
+0048         [~, md5HashMessage]=system(['md5sum "' inputFile '"']);
+0049     case '.exe'
+0050         [~, md5HashMessage]=system(['certutil -hashfile "' inputFile '" MD5"']);
+0051 end
+0052 
+0053 %Extract MD5 hash from a string
+0054 md5Hash = char(regexp(md5HashMessage,'[a-f0-9]{32}','match'));
+0055 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/io/getToolboxVersion.html b/doc/io/getToolboxVersion.html
index ef1b173f..64d98f58 100644
--- a/doc/io/getToolboxVersion.html
+++ b/doc/io/getToolboxVersion.html
@@ -24,7 +24,7 @@ 
    PURPOSE ^getToolboxVersion

    SYNOPSIS ^

    -
    function version = getToolboxVersion(toolbox,fileID,masterFlag)
    +
    function version = getToolboxVersion(toolbox,fileID,mainBranchFlag)

    DESCRIPTION ^

     getToolboxVersion
@@ -34,13 +34,13 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
@@ -49,7 +49,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 </ul>
 This function is called by:
 <ul style=
-
  • exportForGit	exportForGit
    • 
+
  • exportForGit	exportForGit
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -57,7 +57,7 @@ 
    SUBFUNCTIONS ^function slashPos = getSlashPos(path)
 
 
    SOURCE CODE ^
    
-
    0001 function version = getToolboxVersion(toolbox,fileID,masterFlag)
+
    0001 function version = getToolboxVersion(toolbox,fileID,mainBranchFlag)
 0002 % getToolboxVersion
 0003 %   Returns the version of a given toolbox, or if not available the latest
 0004 %   commit hash (7 characters).
@@ -65,16 +65,16 @@ 
    SOURCE CODE ^%   toolbox         string with the toolbox name (e.g. "RAVEN")
 0007 %   fileID          string with the name of a file that is only found in
 0008 %                   the corresponding toolbox (e.g. "ravenCobraWrapper.m").
-0009 %   masterFlag      logical, if true, function will error if the toolbox is
-0010 %                   not on the master branch (opt, default false).
+0009 %   mainBranchFlag      logical, if true, function will error if the toolbox is
+0010 %                   not on the main branch (opt, default false).
 0011 %
 0012 %   version         string containing either the toolbox version or latest
 0013 %                   commit hash (7 characters).
 0014 %
-0015 %   Usage: version = getToolboxVersion(toolbox,fileID,masterFlag)
+0015 %   Usage: version = getToolboxVersion(toolbox,fileID,mainBranchFlag)
 0016 
 0017 if nargin<3
-0018     masterFlag = false;
+0018     mainBranchFlag = false;
 0019 end
 0020 
 0021 currentPath = pwd;
@@ -97,12 +97,12 @@ 
    SOURCE CODE ^' toolbox cannot be found'])
 0039     version = 'unknown';
 0040 end
-0041 %Check if in master:
-0042 if masterFlag
+0041 %Check if in main:
+0042 if mainBranchFlag
 0043     currentBranch = git('rev-parse --abbrev-ref HEAD');
-0044     if ~strcmp(currentBranch,'master')
+0044     if any([strcmp(currentBranch, "main"), strcmp(currentBranch, "master")])
 0045         cd(currentPath);
-0046         error(['ERROR: ' toolbox ' not in master. Check-out the master branch of ' toolbox ' before submitting model for Git.'])
+0046         error(['ERROR: ' toolbox ' not in main (or master) branch. Check-out this branch of ' toolbox ' before submitting model for Git.'])
 0047     end
 0048 end
 0049 %Try to find version file of the toolbox:
diff --git a/doc/io/index.html b/doc/io/index.html
index f17f6cf2..c944a6d6 100644
--- a/doc/io/index.html
+++ b/doc/io/index.html
@@ -19,7 +19,7 @@ 
    Index for io
    
 
 
    Matlab files in this directory:
    
 
-
     SBMLFromExcelSBMLFromExcel 
     addJavaPathsaddJavaPaths 
     checkFileExistencecheckFileExistence 
     cleanSheetcleanSheet 
     closeModelcloseModel 
     exportForGitexportForGit 
     exportModelexportModel 
     exportModelToSIFexportModelToSIF 
     exportToExcelFormatexportToExcelFormat 
     exportToTabDelimitedexportToTabDelimited 
     getFullPathgetFullPath - Get absolute canonical path of a file or folder 
     getToolboxVersiongetToolboxVersion 
     importExcelModelimportExcelModel 
     importModelimportModel 
     loadSheetloadSheet 
     loadWorkbookloadWorkbook 
     startupAdd the Java Paths at startup in order to be ready for use if the Toolbox is on the path 
     writeSheetwriteSheet 
     writeYamlwriteYaml 
    
+     SBMLFromExcelSBMLFromExcel  addJavaPathsaddJavaPaths  checkFileExistencecheckFileExistence  cleanSheetcleanSheet  closeModelcloseModel  exportForGitexportForGit  exportModelexportModel  exportModelToSIFexportModelToSIF  exportToExcelFormatexportToExcelFormat  exportToTabDelimitedexportToTabDelimited  getFullPathgetFullPath - Get absolute canonical path of a file or folder  getMD5HashgetMD5Hash  getToolboxVersiongetToolboxVersion  importExcelModelimportExcelModel  importModelimportModel  loadSheetloadSheet  loadWorkbookloadWorkbook  sortIdentifiersexportModel  startupAdd the Java Paths at startup in order to be ready for use if the Toolbox is on the path  writeSheetwriteSheet  writeYamlwriteYaml 
 
 
 
diff --git a/doc/io/loadWorkbook.html b/doc/io/loadWorkbook.html
index 7c06b146..ebca57da 100644
--- a/doc/io/loadWorkbook.html
+++ b/doc/io/loadWorkbook.html
@@ -46,7 +46,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=addJavaPaths	addJavaPaths
  • getFullPath	getFullPath - Get absolute canonical path of a file or folder
    • 
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
  • importExcelModel	importExcelModel
    • 
 
 
 
diff --git a/doc/io/sortIdentifiers.html b/doc/io/sortIdentifiers.html
new file mode 100644
index 00000000..a65291c6
--- /dev/null
+++ b/doc/io/sortIdentifiers.html
@@ -0,0 +1,83 @@
+
+
+
+  Description of sortIdentifiers
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  io > sortIdentifiers.m
    
+
+
+
+
    sortIdentifiers
+
    
+
+
    PURPOSE ^
    
+
    exportModel
    
+
+
    SYNOPSIS ^
    
+
    function newModel = sortIdentifiers(model) 
    
+
+
    DESCRIPTION ^
    
+
     exportModel
+   Sort reactions, metabolites, genes and compartments alphabetically by
+   their identifier.
+
+   Input:
+   model       a model structure
+
+   Output:
+   newModel    an updated model structure with alphabetically sorted
+               identifiers
+
+   Usage: newModel=sortIdentifiers(model)
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
      
+
    
+This function is called by:
+
+
+
+
+
+
    SOURCE CODE ^
    
+
    0001 function newModel = sortIdentifiers(model)
+0002 % exportModel
+0003 %   Sort reactions, metabolites, genes and compartments alphabetically by
+0004 %   their identifier.
+0005 %
+0006 %   Input:
+0007 %   model       a model structure
+0008 %
+0009 %   Output:
+0010 %   newModel    an updated model structure with alphabetically sorted
+0011 %               identifiers
+0012 %
+0013 %   Usage: newModel=sortIdentifiers(model)
+0014 
+0015 [~,I]=sort(model.rxns);
+0016 newModel=permuteModel(model,I,'rxns');
+0017 [~,I]=sort(newModel.mets);
+0018 newModel=permuteModel(newModel,I,'mets');
+0019 if isfield(newModel,'genes')
+0020     [~,I]=sort(newModel.genes);
+0021     newModel=permuteModel(newModel,I,'genes');
+0022 end
+0023 [~,I]=sort(newModel.comps);
+0024 newModel=permuteModel(newModel,I,'comps');
+0025 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/io/writeSheet.html b/doc/io/writeSheet.html
index 10b1aa8c..04270560 100644
--- a/doc/io/writeSheet.html
+++ b/doc/io/writeSheet.html
@@ -48,7 +48,7 @@ 
    CROSS-REFERENCE INFORMATION ^
 <li><a href=addJavaPaths	addJavaPaths
 This function is called by:
 
+
  • exportToExcelFormat	exportToExcelFormat
    • 
 
 
 
    SUBFUNCTIONS ^
    
diff --git a/doc/io/writeYaml.html b/doc/io/writeYaml.html
index c5a19c29..27868d2f 100644
--- a/doc/io/writeYaml.html
+++ b/doc/io/writeYaml.html
@@ -45,10 +45,10 @@ 
    DESCRIPTION ^CROSS-REFERENCE INFORMATION ^
    
 This function calls:
 
      
-
    
+
  • sortIdentifiers	exportModel
    • 
 This function is called by:
 
+
  • exportForGit	exportForGit
    • 
 
 
 
    SUBFUNCTIONS ^
    
@@ -77,298 +77,282 @@ 
    SOURCE CODE ^if nargin < 4
 0020     sortIds = false;
 0021 end
-0022 
-0023 if ~endsWith(name,{'.yml','.yaml'})
-0024     name = strcat(name,'.yml');
-0025 end
-0026 
-0027 %Check that model is in RAVEN format:
-0028 if isfield(model,'rules')
-0029     model = ravenCobraWrapper(model);
-0030 end
-0031 
-0032 %Simplify Miriam fields:
-0033 if isfield(model,'metMiriams')
-0034     [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
-0035     model.newMetMiriams                             = regexprep(model.newMetMiriams,'^.+/','');
-0036 end
-0037 if isfield(model,'rxnMiriams')
-0038     [model.newRxnMiriams,model.newRxnMiriamNames]   = extractMiriam(model.rxnMiriams);
-0039     model.newRxnMiriams                             = regexprep(model.newRxnMiriams,'^.+/','');
+0022 if ~endsWith(name,{'.yml','.yaml'})
+0023     name = strcat(name,'.yml');
+0024 end
+0025 
+0026 %Check that model is in RAVEN format:
+0027 if isfield(model,'rules')
+0028     model = ravenCobraWrapper(model);
+0029 end
+0030 
+0031 %Sort identifiers alphabetically
+0032 if sortIds == true
+0033     model = sortIdentifiers(model);
+0034 end
+0035 
+0036 %Simplify Miriam fields:
+0037 if isfield(model,'metMiriams')
+0038     [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
+0039     model.newMetMiriams                             = regexprep(model.newMetMiriams,'^.+/','');
 0040 end
-0041 if isfield(model,'geneMiriams')
-0042     [model.newGeneMiriams,model.newGeneMiriamNames] = extractMiriam(model.geneMiriams);
-0043     model.newGeneMiriams                            = regexprep(model.newGeneMiriams,'^.+/','');
+0041 if isfield(model,'rxnMiriams')
+0042     [model.newRxnMiriams,model.newRxnMiriamNames]   = extractMiriam(model.rxnMiriams);
+0043     model.newRxnMiriams                             = regexprep(model.newRxnMiriams,'^.+/','');
 0044 end
-0045 if isfield(model,'compMiriams')
-0046     [model.newCompMiriams,model.newCompMiriamNames] = extractMiriam(model.compMiriams);
-0047     model.newCompMiriams                            = regexprep(model.newCompMiriams,'^.+/','');
+0045 if isfield(model,'geneMiriams')
+0046     [model.newGeneMiriams,model.newGeneMiriamNames] = extractMiriam(model.geneMiriams);
+0047     model.newGeneMiriams                            = regexprep(model.newGeneMiriams,'^.+/','');
 0048 end
-0049 
-0050 %Open file:
-0051 fid = fopen(name,'wt');
-0052 fprintf(fid,'---\n!!omap\n');
+0049 if isfield(model,'compMiriams')
+0050     [model.newCompMiriams,model.newCompMiriamNames] = extractMiriam(model.compMiriams);
+0051     model.newCompMiriams                            = regexprep(model.newCompMiriams,'^.+/','');
+0052 end
 0053 
-0054 %Insert file header (metadata)
-0055 writeMetadata(model,fid);
-0056 
-0057 %Metabolites:
-0058 fprintf(fid,'- metabolites:\n');
-0059 if sortIds==true
-0060     [~,pos] = sort(model.mets);
-0061 else
-0062     pos = 1:numel(model.mets);
-0063 end
-0064 for i = 1:length(model.mets)
-0065     fprintf(fid,'    - !!omap\n');
-0066     writeField(model, fid, 'mets',        'txt', pos(i), '  - id',          preserveQuotes)
-0067     writeField(model, fid, 'metNames',    'txt', pos(i), '  - name',        preserveQuotes)
-0068     writeField(model, fid, 'metComps',    'txt', pos(i), '  - compartment', preserveQuotes)
-0069     writeField(model, fid, 'metFormulas', 'txt', pos(i), '  - formula',     preserveQuotes)
-0070     writeField(model, fid, 'metCharges',  'num', pos(i), '  - charge',      preserveQuotes)
-0071     writeField(model, fid, 'inchis',      'txt', pos(i), '  - inchis',      preserveQuotes)
-0072     writeField(model, fid, 'metMiriams',  'txt', pos(i), '  - annotation',  preserveQuotes)
-0073     writeField(model, fid, 'metFrom',     'txt', pos(i), '  - metFrom',     preserveQuotes)
-0074 end
-0075 
-0076 %Reactions:
-0077 fprintf(fid,'- reactions:\n');
-0078 if sortIds==true
-0079     [~,pos] = sort(model.rxns);
-0080 else
-0081     pos = 1:numel(model.rxns);
-0082 end
-0083 for i = 1:length(model.rxns)
-0084     fprintf(fid,'    - !!omap\n');
-0085     writeField(model, fid, 'rxns',                 'txt', pos(i), '  - id',                    preserveQuotes)
-0086     writeField(model, fid, 'rxnNames',             'txt', pos(i), '  - name',                  preserveQuotes)
-0087     writeField(model, fid, 'S',                    'txt', pos(i), '  - metabolites',           preserveQuotes)
-0088     writeField(model, fid, 'lb',                   'num', pos(i), '  - lower_bound',           preserveQuotes)
-0089     writeField(model, fid, 'ub',                   'num', pos(i), '  - upper_bound',           preserveQuotes)
-0090     writeField(model, fid, 'grRules',              'txt', pos(i), '  - gene_reaction_rule',    preserveQuotes)
-0091     writeField(model, fid, 'rxnFrom',              'txt', pos(i), '  - rxnFrom',               preserveQuotes)
-0092     if model.c(i)~=0
-0093         writeField(model, fid, 'c',                    'num', pos(i), '  - objective_coefficient', preserveQuotes)    
-0094     end
-0095     writeField(model, fid, 'eccodes',              'txt', pos(i), '  - eccodes',               preserveQuotes)
-0096     writeField(model, fid, 'rxnReferences',        'txt', pos(i), '  - references',            preserveQuotes)
-0097     writeField(model, fid, 'subSystems',           'txt', pos(i), '  - subsystem',             preserveQuotes)
-0098     writeField(model, fid, 'rxnMiriams',           'txt', pos(i), '  - annotation',            preserveQuotes)
-0099     writeField(model, fid, 'rxnConfidenceScores',  'num', pos(i), '  - confidence_score',      preserveQuotes)
-0100 end
-0101 
-0102 %Genes:
-0103 fprintf(fid,'- genes:\n');
-0104 if sortIds==true
-0105     [~,pos] = sort(model.genes);
-0106 else
-0107     pos = 1:numel(model.genes);
-0108 end
-0109 for i = 1:length(model.genes)
-0110     fprintf(fid,'    - !!omap\n');
-0111     writeField(model, fid, 'genes',          'txt', pos(i), '  - id',         preserveQuotes)
-0112     writeField(model, fid, 'geneShortNames', 'txt', pos(i), '  - name',       preserveQuotes)
-0113     writeField(model, fid, 'geneMiriams',    'txt', pos(i), '  - annotation', preserveQuotes)
-0114 end
-0115 
-0116 %Compartments:
-0117 fprintf(fid,'- compartments: !!omap\n');
-0118 if sortIds==true
-0119     [~,pos] = sort(model.comps);
-0120 else
-0121     pos = 1:numel(model.comps);
-0122 end
-0123 for i = 1:length(model.comps)
-0124     writeField(model, fid, 'compNames',   'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes)
-0125     writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation',             preserveQuotes)
-0126 end
-0127 
-0128 %Close file:
-0129 fclose(fid);
-0130 
-0131 end
-0132 
-0133 function writeField(model,fid,fieldName,type,pos,name,preserveQuotes)
-0134 %Writes a new line in the yaml file if the field exists and the field is
-0135 %not empty at the correspoinding position. It's recursive for some fields
-0136 %(metMiriams, rxnMiriams, and S)
-0137 
-0138 if isfield(model,fieldName)
-0139     if strcmp(fieldName,'metComps')
-0140         %metComps: write full name
-0141         fieldName = 'comps';
-0142         pos       = model.metComps(pos);
-0143     end
-0144     
-0145     field = eval(['model.' fieldName]);
-0146     
-0147     if strcmp(fieldName,'metMiriams')
-0148         if ~isempty(model.metMiriams{pos})
-0149             fprintf(fid,['    ' name ': !!omap\n']);
-0150             for i=1:size(model.newMetMiriams,2)
-0151                 %'i' represents the different miriam names, e.g.
-0152                 %kegg.compound or chebi
-0153                 if ~isempty(model.newMetMiriams{pos,i})
-0154                     %As during the following writeField call the value of
-0155                     %'i' would be lost, it is temporarily concatenated to
-0156                     %'name' parameter, which will be edited later
-0157                     writeField(model, fid, 'newMetMiriams', 'txt', pos, ['      - ' model.newMetMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0158                 end
-0159             end
-0160         end
-0161         
-0162     elseif strcmp(fieldName,'rxnMiriams')
-0163         if ~isempty(model.rxnMiriams{pos})
-0164             fprintf(fid,['    ' name ': !!omap\n']);
-0165             for i=1:size(model.newRxnMiriams,2)
-0166                 if ~isempty(model.newRxnMiriams{pos,i})
-0167                     writeField(model, fid, 'newRxnMiriams', 'txt', pos, ['      - ' model.newRxnMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0168                 end
-0169             end
-0170         end
-0171         
-0172     elseif strcmp(fieldName,'geneMiriams')
-0173         if ~isempty(model.geneMiriams{pos})
-0174             fprintf(fid,['    ' name ': !!omap\n']);
-0175             for i=1:size(model.newGeneMiriams,2)
-0176                 if ~isempty(model.newGeneMiriams{pos,i})
-0177                     writeField(model, fid, 'newGeneMiriams', 'txt', pos, ['      - ' model.newGeneMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0178                 end
-0179             end
-0180         end
-0181         
-0182     elseif strcmp(fieldName,'compMiriams')
-0183         if ~isempty(model.compMiriams{pos})
-0184             fprintf(fid,['    ' name ': !!omap\n']);
-0185             for i=1:size(model.newCompMiriams,2)
-0186                 if ~isempty(model.newCompMiriams{pos,i})
-0187                     writeField(model, fid, 'newCompMiriams', 'txt', pos, ['      - ' model.newCompMiriamNames{i} '_' num2str(i)], preserveQuotes)
-0188                 end
-0189             end
-0190         end
-0191         
-0192     elseif strcmp(fieldName,'S')
-0193         %S: create header & write each metabolite in a new line
-0194         fprintf(fid,['    ' name ': !!omap\n']);
-0195         if sum(field(:,pos) ~= 0) > 0
-0196             model.mets   = model.mets(field(:,pos) ~= 0);
-0197             model.coeffs = field(field(:,pos) ~= 0,pos);
-0198             %Sort metabolites:
-0199             [model.mets,order] = sort(model.mets);
-0200             model.coeffs       = model.coeffs(order);
-0201             for i = 1:length(model.mets)
-0202                 writeField(model, fid, 'coeffs',  'num', i, ['      - ' model.mets{i}], preserveQuotes)
-0203             end
-0204         end
-0205         
-0206     elseif sum(strcmp({'subSystems','newMetMiriams','newRxnMiriams','newGeneMiriams','newCompMiriams','eccodes'},fieldName)) > 0
-0207         %eccodes/rxnNotes: if 1 write in 1 line, if more create header and list
-0208         if strcmp(fieldName,'subSystems')
-0209             list = field{pos};  %subSystems already comes in a cell array
-0210         elseif strcmp(fieldName,'newMetMiriams')
-0211             index = str2double(regexprep(name,'^.+_',''));
-0212             name  = regexprep(name,'_\d+$','');
-0213             list = strsplit(model.newMetMiriams{pos,index},'; ');
-0214         elseif strcmp(fieldName,'newRxnMiriams')
-0215             index = str2double(regexprep(name,'^.+_',''));
-0216             name  = regexprep(name,'_\d+$','');
-0217             list = strsplit(model.newRxnMiriams{pos,index},'; ');
-0218         elseif strcmp(fieldName,'newGeneMiriams')
-0219             index = str2double(regexprep(name,'^.+_',''));
-0220             name  = regexprep(name,'_\d+$','');
-0221             list = strsplit(model.newGeneMiriams{pos,index},'; ');
-0222         elseif strcmp(fieldName,'newCompMiriams')
-0223             index = str2double(regexprep(name,'^.+_',''));
-0224             name  = regexprep(name,'_\d+$','');
-0225             list = strsplit(model.newCompMiriams{pos,index},'; ');
-0226         else
-0227             list = strrep(field{pos},' ','');     %Exception for eccodes
-0228             list = strsplit(list,';');
-0229         end
-0230 
-0231         if length(list) == 1 && ~strcmp(list{1},'') && ~strcmp(fieldName,'subSystems')
-0232             if preserveQuotes
-0233                 list = strcat('"',list,'"');
-0234             end
-0235             fprintf(fid,['    ' name ': ' list{1} '\n']);
-0236         elseif length(list) > 1 || strcmp(fieldName,'subSystems')
-0237             if preserveQuotes
-0238                 list = strcat('"',list,'"');
-0239             end
-0240             fprintf(fid,['    ' name ':\n']);
-0241             for i = 1:length(list)
-0242                 fprintf(fid,[regexprep(name,'(^\s*).*','$1') '        - ' list{i} '\n']);
-0243             end
-0244         end
-0245         
-0246     elseif sum(pos) > 0
-0247         %All other fields:
-0248         if strcmp(type,'txt')
-0249             value = field{pos};
-0250             if preserveQuotes && ~isempty(value)
-0251                 value = strcat('"',value,'"');
-0252             end
-0253         elseif strcmp(type,'num')
-0254             if isnan(field(pos))
-0255                 value = [];
-0256             else
-0257                 value = num2str(field(pos),12);
-0258             end
-0259         end
-0260         if ~isempty(value)
-0261             fprintf(fid,['    ' name ': ' value '\n']);
-0262         end
-0263     end
-0264 end
-0265 
-0266 
-0267 end
-0268 
-0269 function writeMetadata(model,fid)
-0270 % Writes model metadata to the yaml file. This information will eventually
-0271 % be extracted entirely from the model, but for now, many of the entries
-0272 % are hard-coded defaults for HumanGEM.
-0273 
-0274 fprintf(fid, '- metaData:\n');
-0275 fprintf(fid, ['    id: "',          model.id,          '"\n']);
-0276 fprintf(fid, ['    name: "',        model.name, '"\n']);
-0277 if isfield(model,'version')
-0278     fprintf(fid, ['    version: "', model.version,     '"\n']);
-0279 end
-0280 fprintf(fid, ['    date: "',        datestr(now,29),   '"\n']);  % 29=YYYY-MM-DD
-0281 if isfield(model,'annotation')
-0282     if isfield(model.annotation,'defaultLB')
-0283         fprintf(fid, ['    defaultLB: "',    num2str(model.annotation.defaultLB), '"\n']);
-0284     end
-0285     if isfield(model.annotation,'defaultUB')
-0286         fprintf(fid, ['    defaultUB: "',    num2str(model.annotation.defaultUB), '"\n']);
-0287     end
-0288     if isfield(model.annotation,'givenName')
-0289         fprintf(fid, ['    givenName: "',    model.annotation.givenName,          '"\n']);
-0290     end
-0291     if isfield(model.annotation,'familyName')
-0292         fprintf(fid, ['    familyName: "',   model.annotation.familyName,         '"\n']);
-0293     end
-0294     if isfield(model.annotation,'authors')
-0295         fprintf(fid, ['    authors: "',      model.annotation.authors,            '"\n']);
-0296     end
-0297     if isfield(model.annotation,'email')
-0298         fprintf(fid, ['    email: "',        model.annotation.email,              '"\n']);
-0299     end
-0300     if isfield(model.annotation,'organization')
-0301         fprintf(fid, ['    organization: "', model.annotation.organization,       '"\n']);
-0302     end
-0303     if isfield(model.annotation,'taxonomy')
-0304         fprintf(fid, ['    taxonomy: "',     model.annotation.taxonomy,           '"\n']);
-0305     end
-0306     if isfield(model.annotation,'note')
-0307         fprintf(fid, ['    note: "',         model.annotation.note,               '"\n']);
-0308     end
-0309     if isfield(model.annotation,'sourceUrl')
-0310         fprintf(fid, ['    sourceUrl: "',    model.annotation.sourceUrl,          '"\n']);
-0311     end
-0312 end
-0313 end
    
+0054 %Open file:
+0055 fid = fopen(name,'wt');
+0056 fprintf(fid,'---\n!!omap\n');
+0057 
+0058 %Insert file header (metadata)
+0059 writeMetadata(model,fid);
+0060 
+0061 %Metabolites:
+0062 fprintf(fid,'- metabolites:\n');
+0063 for i = 1:length(model.mets)
+0064     fprintf(fid,'    - !!omap\n');
+0065     writeField(model, fid, 'mets',        'txt', pos(i), '  - id',          preserveQuotes)
+0066     writeField(model, fid, 'metNames',    'txt', pos(i), '  - name',        preserveQuotes)
+0067     writeField(model, fid, 'metComps',    'txt', pos(i), '  - compartment', preserveQuotes)
+0068     writeField(model, fid, 'metFormulas', 'txt', pos(i), '  - formula',     preserveQuotes)
+0069     writeField(model, fid, 'metCharges',  'num', pos(i), '  - charge',      preserveQuotes)
+0070     writeField(model, fid, 'inchis',      'txt', pos(i), '  - inchis',      preserveQuotes)
+0071     writeField(model, fid, 'metMiriams',  'txt', pos(i), '  - annotation',  preserveQuotes)
+0072     writeField(model, fid, 'metFrom',     'txt', pos(i), '  - metFrom',     preserveQuotes)
+0073 end
+0074 
+0075 %Reactions:
+0076 fprintf(fid,'- reactions:\n');
+0077 for i = 1:length(model.rxns)
+0078     fprintf(fid,'    - !!omap\n');
+0079     writeField(model, fid, 'rxns',                 'txt', pos(i), '  - id',                    preserveQuotes)
+0080     writeField(model, fid, 'rxnNames',             'txt', pos(i), '  - name',                  preserveQuotes)
+0081     writeField(model, fid, 'S',                    'txt', pos(i), '  - metabolites',           preserveQuotes)
+0082     writeField(model, fid, 'lb',                   'num', pos(i), '  - lower_bound',           preserveQuotes)
+0083     writeField(model, fid, 'ub',                   'num', pos(i), '  - upper_bound',           preserveQuotes)
+0084     writeField(model, fid, 'grRules',              'txt', pos(i), '  - gene_reaction_rule',    preserveQuotes)
+0085     writeField(model, fid, 'rxnFrom',              'txt', pos(i), '  - rxnFrom',               preserveQuotes)
+0086     if model.c(i)~=0
+0087         writeField(model, fid, 'c',                    'num', pos(i), '  - objective_coefficient', preserveQuotes)    
+0088     end
+0089     writeField(model, fid, 'eccodes',              'txt', pos(i), '  - eccodes',               preserveQuotes)
+0090     writeField(model, fid, 'rxnReferences',        'txt', pos(i), '  - references',            preserveQuotes)
+0091     writeField(model, fid, 'subSystems',           'txt', pos(i), '  - subsystem',             preserveQuotes)
+0092     writeField(model, fid, 'rxnMiriams',           'txt', pos(i), '  - annotation',            preserveQuotes)
+0093     writeField(model, fid, 'rxnConfidenceScores',  'num', pos(i), '  - confidence_score',      preserveQuotes)
+0094 end
+0095 
+0096 %Genes:
+0097 fprintf(fid,'- genes:\n');
+0098 for i = 1:length(model.genes)
+0099     fprintf(fid,'    - !!omap\n');
+0100     writeField(model, fid, 'genes',          'txt', pos(i), '  - id',         preserveQuotes)
+0101     writeField(model, fid, 'geneShortNames', 'txt', pos(i), '  - name',       preserveQuotes)
+0102     writeField(model, fid, 'geneMiriams',    'txt', pos(i), '  - annotation', preserveQuotes)
+0103 end
+0104 
+0105 %Compartments:
+0106 fprintf(fid,'- compartments: !!omap\n');
+0107 for i = 1:length(model.comps)
+0108     writeField(model, fid, 'compNames',   'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes)
+0109     writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation',             preserveQuotes)
+0110 end
+0111 
+0112 %Close file:
+0113 fclose(fid);
+0114 
+0115 end
+0116 
+0117 function writeField(model,fid,fieldName,type,pos,name,preserveQuotes)
+0118 %Writes a new line in the yaml file if the field exists and the field is
+0119 %not empty at the correspoinding position. It's recursive for some fields
+0120 %(metMiriams, rxnMiriams, and S)
+0121 
+0122 if isfield(model,fieldName)
+0123     if strcmp(fieldName,'metComps')
+0124         %metComps: write full name
+0125         fieldName = 'comps';
+0126         pos       = model.metComps(pos);
+0127     end
+0128     
+0129     field = eval(['model.' fieldName]);
+0130     
+0131     if strcmp(fieldName,'metMiriams')
+0132         if ~isempty(model.metMiriams{pos})
+0133             fprintf(fid,['    ' name ': !!omap\n']);
+0134             for i=1:size(model.newMetMiriams,2)
+0135                 %'i' represents the different miriam names, e.g.
+0136                 %kegg.compound or chebi
+0137                 if ~isempty(model.newMetMiriams{pos,i})
+0138                     %As during the following writeField call the value of
+0139                     %'i' would be lost, it is temporarily concatenated to
+0140                     %'name' parameter, which will be edited later
+0141                     writeField(model, fid, 'newMetMiriams', 'txt', pos, ['      - ' model.newMetMiriamNames{i} '_' num2str(i)], preserveQuotes)
+0142                 end
+0143             end
+0144         end
+0145         
+0146     elseif strcmp(fieldName,'rxnMiriams')
+0147         if ~isempty(model.rxnMiriams{pos})
+0148             fprintf(fid,['    ' name ': !!omap\n']);
+0149             for i=1:size(model.newRxnMiriams,2)
+0150                 if ~isempty(model.newRxnMiriams{pos,i})
+0151                     writeField(model, fid, 'newRxnMiriams', 'txt', pos, ['      - ' model.newRxnMiriamNames{i} '_' num2str(i)], preserveQuotes)
+0152                 end
+0153             end
+0154         end
+0155         
+0156     elseif strcmp(fieldName,'geneMiriams')
+0157         if ~isempty(model.geneMiriams{pos})
+0158             fprintf(fid,['    ' name ': !!omap\n']);
+0159             for i=1:size(model.newGeneMiriams,2)
+0160                 if ~isempty(model.newGeneMiriams{pos,i})
+0161                     writeField(model, fid, 'newGeneMiriams', 'txt', pos, ['      - ' model.newGeneMiriamNames{i} '_' num2str(i)], preserveQuotes)
+0162                 end
+0163             end
+0164         end
+0165         
+0166     elseif strcmp(fieldName,'compMiriams')
+0167         if ~isempty(model.compMiriams{pos})
+0168             fprintf(fid,['    ' name ': !!omap\n']);
+0169             for i=1:size(model.newCompMiriams,2)
+0170                 if ~isempty(model.newCompMiriams{pos,i})
+0171                     writeField(model, fid, 'newCompMiriams', 'txt', pos, ['      - ' model.newCompMiriamNames{i} '_' num2str(i)], preserveQuotes)
+0172                 end
+0173             end
+0174         end
+0175         
+0176     elseif strcmp(fieldName,'S')
+0177         %S: create header & write each metabolite in a new line
+0178         fprintf(fid,['    ' name ': !!omap\n']);
+0179         if sum(field(:,pos) ~= 0) > 0
+0180             model.mets   = model.mets(field(:,pos) ~= 0);
+0181             model.coeffs = field(field(:,pos) ~= 0,pos);
+0182             %Sort metabolites:
+0183             [model.mets,order] = sort(model.mets);
+0184             model.coeffs       = model.coeffs(order);
+0185             for i = 1:length(model.mets)
+0186                 writeField(model, fid, 'coeffs',  'num', i, ['      - ' model.mets{i}], preserveQuotes)
+0187             end
+0188         end
+0189         
+0190     elseif sum(strcmp({'subSystems','newMetMiriams','newRxnMiriams','newGeneMiriams','newCompMiriams','eccodes'},fieldName)) > 0
+0191         %eccodes/rxnNotes: if 1 write in 1 line, if more create header and list
+0192         if strcmp(fieldName,'subSystems')
+0193             list = field{pos};  %subSystems already comes in a cell array
+0194         elseif strcmp(fieldName,'newMetMiriams')
+0195             index = str2double(regexprep(name,'^.+_',''));
+0196             name  = regexprep(name,'_\d+$','');
+0197             list = strsplit(model.newMetMiriams{pos,index},'; ');
+0198         elseif strcmp(fieldName,'newRxnMiriams')
+0199             index = str2double(regexprep(name,'^.+_',''));
+0200             name  = regexprep(name,'_\d+$','');
+0201             list = strsplit(model.newRxnMiriams{pos,index},'; ');
+0202         elseif strcmp(fieldName,'newGeneMiriams')
+0203             index = str2double(regexprep(name,'^.+_',''));
+0204             name  = regexprep(name,'_\d+$','');
+0205             list = strsplit(model.newGeneMiriams{pos,index},'; ');
+0206         elseif strcmp(fieldName,'newCompMiriams')
+0207             index = str2double(regexprep(name,'^.+_',''));
+0208             name  = regexprep(name,'_\d+$','');
+0209             list = strsplit(model.newCompMiriams{pos,index},'; ');
+0210         else
+0211             list = strrep(field{pos},' ','');     %Exception for eccodes
+0212             list = strsplit(list,';');
+0213         end
+0214 
+0215         if length(list) == 1 && ~strcmp(list{1},'') && ~strcmp(fieldName,'subSystems')
+0216             if preserveQuotes
+0217                 list = strcat('"',list,'"');
+0218             end
+0219             fprintf(fid,['    ' name ': ' list{1} '\n']);
+0220         elseif length(list) > 1 || strcmp(fieldName,'subSystems')
+0221             if preserveQuotes
+0222                 list = strcat('"',list,'"');
+0223             end
+0224             fprintf(fid,['    ' name ':\n']);
+0225             for i = 1:length(list)
+0226                 fprintf(fid,[regexprep(name,'(^\s*).*','$1') '        - ' list{i} '\n']);
+0227             end
+0228         end
+0229         
+0230     elseif sum(pos) > 0
+0231         %All other fields:
+0232         if strcmp(type,'txt')
+0233             value = field{pos};
+0234             if preserveQuotes && ~isempty(value)
+0235                 value = strcat('"',value,'"');
+0236             end
+0237         elseif strcmp(type,'num')
+0238             if isnan(field(pos))
+0239                 value = [];
+0240             else
+0241                 value = num2str(field(pos),12);
+0242             end
+0243         end
+0244         if ~isempty(value)
+0245             fprintf(fid,['    ' name ': ' value '\n']);
+0246         end
+0247     end
+0248 end
+0249 
+0250 
+0251 end
+0252 
+0253 function writeMetadata(model,fid)
+0254 % Writes model metadata to the yaml file. This information will eventually
+0255 % be extracted entirely from the model, but for now, many of the entries
+0256 % are hard-coded defaults for HumanGEM.
+0257 
+0258 fprintf(fid, '- metaData:\n');
+0259 fprintf(fid, ['    id: "',          model.id,          '"\n']);
+0260 fprintf(fid, ['    name: "',        model.name, '"\n']);
+0261 if isfield(model,'version')
+0262     fprintf(fid, ['    version: "', model.version,     '"\n']);
+0263 end
+0264 fprintf(fid, ['    date: "',        datestr(now,29),   '"\n']);  % 29=YYYY-MM-DD
+0265 if isfield(model,'annotation')
+0266     if isfield(model.annotation,'defaultLB')
+0267         fprintf(fid, ['    defaultLB: "',    num2str(model.annotation.defaultLB), '"\n']);
+0268     end
+0269     if isfield(model.annotation,'defaultUB')
+0270         fprintf(fid, ['    defaultUB: "',    num2str(model.annotation.defaultUB), '"\n']);
+0271     end
+0272     if isfield(model.annotation,'givenName')
+0273         fprintf(fid, ['    givenName: "',    model.annotation.givenName,          '"\n']);
+0274     end
+0275     if isfield(model.annotation,'familyName')
+0276         fprintf(fid, ['    familyName: "',   model.annotation.familyName,         '"\n']);
+0277     end
+0278     if isfield(model.annotation,'authors')
+0279         fprintf(fid, ['    authors: "',      model.annotation.authors,            '"\n']);
+0280     end
+0281     if isfield(model.annotation,'email')
+0282         fprintf(fid, ['    email: "',        model.annotation.email,              '"\n']);
+0283     end
+0284     if isfield(model.annotation,'organization')
+0285         fprintf(fid, ['    organization: "', model.annotation.organization,       '"\n']);
+0286     end
+0287     if isfield(model.annotation,'taxonomy')
+0288         fprintf(fid, ['    taxonomy: "',     model.annotation.taxonomy,           '"\n']);
+0289     end
+0290     if isfield(model.annotation,'note')
+0291         fprintf(fid, ['    note: "',         model.annotation.note,               '"\n']);
+0292     end
+0293     if isfield(model.annotation,'sourceUrl')
+0294         fprintf(fid, ['    sourceUrl: "',    model.annotation.sourceUrl,          '"\n']);
+0295     end
+0296 end
+0297 end
    
 
    Generated by m2html © 2005
    
 
 
\ No newline at end of file
diff --git a/doc/testing/index.html b/doc/testing/index.html
deleted file mode 100644
index e9dab614..00000000
--- a/doc/testing/index.html
+++ /dev/null
@@ -1,31 +0,0 @@
-
-
-
-  Index for Directory testing
-  
-  
-  
-  
-  
-  
-
-
-
-
-
    < Master indexIndex for testing >
    
-
-
    Index for testing
    
-
-
    Matlab files in this directory:
    
-
-
     testBlasttestBlast 
     testDiamondtestDiamond 
    
-
-
-
    Subsequent directories:
    
-
-
-
    Generated by m2html © 2005
    
-
-
\ No newline at end of file
diff --git a/doc/testing/testBlast.html b/doc/testing/testBlast.html
deleted file mode 100644
index e0b78733..00000000
--- a/doc/testing/testBlast.html
+++ /dev/null
@@ -1,189 +0,0 @@
-
-
-
-  Description of testBlast
-  
-  
-  
-  
-  
-  
-
-
-
-
    Home >  testing > testBlast.m
    
-
-
-
-
    testBlast
-
    
-
-
    PURPOSE ^
    
-
    testBlast
    
-
-
    SYNOPSIS ^
    
-
    function [success,blastStructure]=testBlast(fullCheck) 
    
-
-
    DESCRIPTION ^
    
-
     testBlast
-   Performs a check for BLAST+ functionality in RAVEN. Depending on the
-   parameter settings the user can choose between a quick check for
-   binaries or the thorough testing while building BLAST database and
-   running homology search with BLASTP
-
-   Input:
-   fullCheck       true if the thorough BLAST+ testing should be performed
-                   (opt, default true)
-
-   Output: 
-   success         true if the test was successful, otherwise equal to
-                   zero
-   blastStructure    blastStructure resulting from the thorough BLAST+ check
-
-   NOTE: The purpose of the thorough check is to assess whether the
-   homology search can be successfully performed using existing BLAST+
-   binaries. This testing function is completely standalone, only
-   requiring BLAST+ binaries and multi-FASTA file sce.fa from tutorials
-   directory
-
-   Usage: [success,blastStructure]=testBlast(fullCheck)
    
-
-
-
    CROSS-REFERENCE INFORMATION ^
    
-This function calls:
-
-This function is called by:
-
-
-
-
-
-
    SOURCE CODE ^
    
-
    0001 function [success,blastStructure]=testBlast(fullCheck)
-0002 % testBlast
-0003 %   Performs a check for BLAST+ functionality in RAVEN. Depending on the
-0004 %   parameter settings the user can choose between a quick check for
-0005 %   binaries or the thorough testing while building BLAST database and
-0006 %   running homology search with BLASTP
-0007 %
-0008 %   Input:
-0009 %   fullCheck       true if the thorough BLAST+ testing should be performed
-0010 %                   (opt, default true)
-0011 %
-0012 %   Output:
-0013 %   success         true if the test was successful, otherwise equal to
-0014 %                   zero
-0015 %   blastStructure    blastStructure resulting from the thorough BLAST+ check
-0016 %
-0017 %   NOTE: The purpose of the thorough check is to assess whether the
-0018 %   homology search can be successfully performed using existing BLAST+
-0019 %   binaries. This testing function is completely standalone, only
-0020 %   requiring BLAST+ binaries and multi-FASTA file sce.fa from tutorials
-0021 %   directory
-0022 %
-0023 %   Usage: [success,blastStructure]=testBlast(fullCheck)
-0024 
-0025 if nargin<1
-0026     fullCheck=true;
-0027 end
-0028 
-0029 %Get the directory for RAVEN Toolbox
-0030 [ST, I]=dbstack('-completenames');
-0031 ravenPath=fileparts(fileparts(ST(I).file));
-0032 
-0033 if isunix
-0034     if ismac
-0035         binEnd='.mac';
-0036     else
-0037         binEnd='';
-0038     end
-0039 elseif ispc
-0040     binEnd='';
-0041     setenv('BLASTDB_LMDB_MAP_SIZE','1000000');
-0042 else
-0043     dispEM('Unknown OS, exiting.')
-0044     return
-0045 end
-0046 
-0047 %Create an empty blastStructure. Even if a quick BLAST+ evaluation is
-0048 %considered, blastStructure should still be in the output
-0049 blastStructure=[];
-0050 
-0051 if ~fullCheck
-0052     fprintf(['Checking blastp' binEnd '... ']);
-0053     [res,~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '"']);
-0054     if res==1
-0055         fprintf('OK\n');
-0056     else
-0057         fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-0058     end
-0059     fprintf(['Checking makeblastdb' binEnd '... ']);
-0060     [res,~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '"']);
-0061     if res==1
-0062         fprintf('OK\n');
-0063     else
-0064         fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-0065     end
-0066 else    
-0067     %Generate temporary names for working directory and outFile
-0068     tmpDB=tempname;
-0069     outFile=tempname;
-0070     
-0071     %Run BLAST multi-threaded to use all logical cores assigned to MATLAB
-0072     cores = evalc('feature(''numcores'')');
-0073     cores = strsplit(cores, 'MATLAB was assigned: ');
-0074     cores = regexp(cores{2},'^\d*','match');
-0075     cores = cores{1};
-0076     
-0077     %Create a temporary folder and copy multi-FASTA file there
-0078     [~, ~]=system(['mkdir "' tmpDB '"']);
-0079     copyfile(fullfile(ravenPath,'tutorial','sce.fa'),tmpDB);
-0080     
-0081     %Construct a BLAST database
-0082     fprintf('Testing makeblastdb... ');
-0083     [res, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' fullfile(tmpDB,'sce.fa') '" -out "' tmpDB '" -dbtype prot']);
-0084     if res~=0
-0085         fprintf('Not OK\n');
-0086         EM=['makeblastdb did not run successfully, error: ', num2str(res)];
-0087         dispEM(EM,true);
-0088     end
-0089     fprintf('OK\n');
-0090     
-0091     %Run a homology search
-0092     fprintf('Testing blastp... ');
-0093     [res, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' fullfile(tmpDB,'sce.fa') '" -out "' outFile '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
-0094     if res~=0
-0095         fprintf('Not OK\n');
-0096         EM=['blastp did not run successfully, error: ', num2str(res)];
-0097         dispEM(EM,true);
-0098     end
-0099     fprintf('OK\n');
-0100     
-0101     %Remove temporary folder, since homology search is finished
-0102     [~, ~]=system(['rm "' tmpDB '" -r']);
-0103     
-0104     %Done with the BLAST, do the parsing of the text file
-0105     blastStructure.fromId='sce';
-0106     blastStructure.toId='sco';
-0107     A=readtable(outFile,'Delimiter',',','Format','%s%s%f%f%f%f%f');
-0108     blastStructure.fromGenes=A{:,1};
-0109     blastStructure.toGenes=A{:,2};
-0110     blastStructure.evalue=table2array(A(:,3));
-0111     blastStructure.identity=table2array(A(:,4));
-0112     blastStructure.aligLen=table2array(A(:,5));
-0113     blastStructure.bitscore=table2array(A(:,6));
-0114     blastStructure.ppos=table2array(A(:,7));
-0115     
-0116     %Remove the old tempfiles
-0117     delete([outFile '*']);
-0118 end
-0119 
-0120 success=1;
-0121 end
    
-
    Generated by m2html © 2005
    
-
-
\ No newline at end of file
diff --git a/doc/testing/testDiamond.html b/doc/testing/testDiamond.html
deleted file mode 100644
index 3e9aa29e..00000000
--- a/doc/testing/testDiamond.html
+++ /dev/null
@@ -1,181 +0,0 @@
-
-
-
-  Description of testDiamond
-  
-  
-  
-  
-  
-  
-
-
-
-
    Home >  testing > testDiamond.m
    
-
-
-
-
    testDiamond
-
    
-
-
    PURPOSE ^
    
-
    testDiamond
    
-
-
    SYNOPSIS ^
    
-
    function [success,blastStructure]=testDiamond(fullCheck) 
    
-
-
    DESCRIPTION ^
    
-
     testDiamond
-   Performs a check for DIAMOND functionality in RAVEN. Depending on the
-   parameter settings the user can choose between a quick check for
-   binaries or the thorough testing while building DIAMOND database and
-   running homology search with DIAMOND
-
-   Input:
-   fullCheck       true if the thorough DIAMOND testing should be
-                   performed (opt, default true)
-
-   Output: 
-   success         true if the test was successful, otherwise equal to
-                   zero
-   blastStructure    blastStructure resulting from the thorough BLAST+ check
-
-   NOTE: The purpose of the thorough check is to assess whether the
-   homology search can be successfully performed using existing BLAST+
-   binaries. This testing function is completely standalone, only
-   requiring DIAMOND binary and multi-FASTA file sce.fa from tutorials
-   directory
-
-   Usage: [success,blastStructure]=testDiamond(fullCheck)
    
-
-
-
    CROSS-REFERENCE INFORMATION ^
    
-This function calls:
-
-This function is called by:
-
-
-
-
-
-
    SOURCE CODE ^
    
-
    0001 function [success,blastStructure]=testDiamond(fullCheck)
-0002 % testDiamond
-0003 %   Performs a check for DIAMOND functionality in RAVEN. Depending on the
-0004 %   parameter settings the user can choose between a quick check for
-0005 %   binaries or the thorough testing while building DIAMOND database and
-0006 %   running homology search with DIAMOND
-0007 %
-0008 %   Input:
-0009 %   fullCheck       true if the thorough DIAMOND testing should be
-0010 %                   performed (opt, default true)
-0011 %
-0012 %   Output:
-0013 %   success         true if the test was successful, otherwise equal to
-0014 %                   zero
-0015 %   blastStructure    blastStructure resulting from the thorough BLAST+ check
-0016 %
-0017 %   NOTE: The purpose of the thorough check is to assess whether the
-0018 %   homology search can be successfully performed using existing BLAST+
-0019 %   binaries. This testing function is completely standalone, only
-0020 %   requiring DIAMOND binary and multi-FASTA file sce.fa from tutorials
-0021 %   directory
-0022 %
-0023 %   Usage: [success,blastStructure]=testDiamond(fullCheck)
-0024 
-0025 if nargin<1
-0026     fullCheck=true;
-0027 end
-0028 
-0029 %Get the directory for RAVEN Toolbox
-0030 [ST, I]=dbstack('-completenames');
-0031 ravenPath=fileparts(fileparts(ST(I).file));
-0032 
-0033 if isunix
-0034     if ismac
-0035         binEnd='.mac';
-0036     else
-0037         binEnd='';
-0038     end
-0039 elseif ispc
-0040     binEnd='';
-0041 else
-0042     dispEM('Unknown OS, exiting.')
-0043     return
-0044 end
-0045 
-0046 %Create an empty blastStructure. Even if a quick DIAMOND evaluation is
-0047 %considered, blastStructure should still be in the output
-0048 blastStructure=[];
-0049 
-0050 if ~fullCheck
-0051     fprintf(['Checking diamond' binEnd '... ']);
-0052     [res,~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '"']);
-0053     if res==1
-0054         fprintf('OK\n');
-0055     else
-0056         fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-0057     end
-0058 else    
-0059     %Generate temporary names for working directory and outFile
-0060     tmpDB=tempname;
-0061     outFile=tempname;
-0062     
-0063     %Run DIAMOND multi-threaded to use all logical cores assigned to MATLAB
-0064     cores = evalc('feature(''numcores'')');
-0065     cores = strsplit(cores, 'MATLAB was assigned: ');
-0066     cores = regexp(cores{2},'^\d*','match');
-0067     cores = cores{1};
-0068     
-0069     %Create a temporary folder and copy multi-FASTA file there
-0070     [~, ~]=system(['mkdir "' tmpDB '"']);
-0071     copyfile(fullfile(ravenPath,'tutorial','sce.fa'),tmpDB);
-0072     
-0073     %Construct a DIAMOND database
-0074     fprintf('Testing DIAMOND makedb... ');
-0075     [res, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fullfile(tmpDB,'sce.fa') '" --db "' tmpDB '"']);
-0076     if res~=0
-0077         fprintf('Not OK\n');
-0078         EM=['DIAMOND makedb did not run successfully, error: ', num2str(res)];
-0079         dispEM(EM,true);
-0080     end
-0081     fprintf('OK\n');
-0082     
-0083     %Run a homology search
-0084     fprintf('Testing DIAMOND blastp... ');
-0085     [res, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fullfile(tmpDB,'sce.fa') '" --out "' outFile '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
-0086     if res~=0
-0087         fprintf('Not OK\n');
-0088         EM=['DIAMOND blastp did not run successfully, error: ', num2str(res)];
-0089         dispEM(EM,true);
-0090     end
-0091     fprintf('OK\n');
-0092     
-0093     %Remove temporary folder, since homology search is finished
-0094     [~, ~]=system(['rm "' tmpDB '" -r']);
-0095     
-0096     %Done with the DIAMOND, do the parsing of the text file
-0097     blastStructure.fromId='sce';
-0098     blastStructure.toId='sco';
-0099     A=readtable(outFile,'Delimiter','\t','Format','%s%s%f%f%f%f%f');
-0100     blastStructure.fromGenes=A{:,1};
-0101     blastStructure.toGenes=A{:,2};
-0102     blastStructure.evalue=table2array(A(:,3));
-0103     blastStructure.identity=table2array(A(:,4));
-0104     blastStructure.aligLen=table2array(A(:,5));
-0105     blastStructure.bitscore=table2array(A(:,6));
-0106     blastStructure.ppos=table2array(A(:,7));
-0107     
-0108     %Remove the old tempfiles
-0109     delete([outFile '*']);
-0110 end
-0111 
-0112 success=1;
-0113 end
    
-
    Generated by m2html © 2005
    
-
-
\ No newline at end of file
diff --git a/doc/testing/unit_tests/blastPlusTests.html b/doc/testing/unit_tests/blastPlusTests.html
new file mode 100644
index 00000000..2b0ba05b
--- /dev/null
+++ b/doc/testing/unit_tests/blastPlusTests.html
@@ -0,0 +1,108 @@
+
+
+
+  Description of blastPlusTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > blastPlusTests.m
    
+
+
+
+
    blastPlusTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = blastPlusTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('blastPlusTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('blastPlusTests.m')
+0003 function tests = blastPlusTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function testBlastPlus(testCase)
+0008 %This unit test comprises several functionality tests for BLAST+ in RAVEN:
+0009 % 1. MD5 checksum check for BLAST database files. This check is applied for
+0010 %    "phr", "pot", "psq" and "pto" files. The remaining files (i.e. "pdb",
+0011 %    "pin" and "ptf") are not compared as these seem to be
+0012 %    machine-specific.
+0013 % 2. Non-parsed text check for BLAST result files. Although the content of
+0014 %    the files is exactly the same, their MD5 hashes are somehow different
+0015 %    between the operating systems.
+0016 % 3. Check of resulting blastStructure against the expected one. This is
+0017 %    done to test BLAST results parsing in RAVEN.
+0018 
+0019 %%
+0020 %Get the directory for RAVEN Toolbox
+0021 [ST, I]=dbstack('-completenames');
+0022 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0023 
+0024 %Import structures that contain expected MD5 hashes and BLAST results
+0025 sourceDir = fileparts(which(mfilename));
+0026 load([sourceDir,'/test_data/expBlastResults.mat'],'expBlastStructure','expBlastReport');
+0027 
+0028 organismID='sce';
+0029 fastaFile=fullfile(ravenPath,'testing','unit_tests','test_data','yeast_galactosidases.fa');
+0030 modelIDs={'hsa' 'afv'};
+0031 refFastaFiles={fullfile(ravenPath,'testing','unit_tests','test_data','human_galactosidases.fa') fullfile(ravenPath,'testing','unit_tests','test_data','aflavus_galactosidases.fa')};
+0032 
+0033 %%
+0034 %Run BLAST
+0035 [actBlastStructure,actBlastReport]=getBlast(organismID,fastaFile,modelIDs,refFastaFiles,true,true);
+0036 
+0037 %%
+0038 %Test 1a: Check if MD5 checksums for BLAST database files are the same
+0039 verifyEqual(testCase,actBlastReport.dbHashes,expBlastReport.dbHashes);
+0040 
+0041 %Test 1b: Change one of the MD5 checksums and check if test fails
+0042 actBlastReport.dbHashes.phr{1,1}=actBlastReport.dbHashes.phr{1,2};
+0043 verifyNotEqual(testCase,actBlastReport.dbHashes,expBlastReport.dbHashes);
+0044 
+0045 %Test 2a: Check if BLAST result files are the same
+0046 verifyEqual(testCase,actBlastReport.blastTxtOutput,expBlastReport.blastTxtOutput);
+0047 
+0048 %Test 2b: Change actual BLAST result file and check if test fails
+0049 actBlastReport.blastTxtOutput='empty';
+0050 verifyNotEqual(testCase,actBlastReport.blastTxtOutput,expBlastReport.blastTxtOutput);
+0051 
+0052 %Test 3a: Check if BLAST structures are the same
+0053 verifyEqual(testCase,actBlastStructure,expBlastStructure);
+0054 
+0055 %Test 3b: Modify actual BLAST structure and check if test fails
+0056 actBlastStructure(1,1).toId=actBlastStructure(1,1).fromId;
+0057 verifyNotEqual(testCase,actBlastStructure,expBlastStructure);
+0058 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/cdhitTests.html b/doc/testing/unit_tests/cdhitTests.html
new file mode 100644
index 00000000..c2a87baa
--- /dev/null
+++ b/doc/testing/unit_tests/cdhitTests.html
@@ -0,0 +1,130 @@
+
+
+
+  Description of cdhitTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > cdhitTests.m
    
+
+
+
+
    cdhitTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = cdhitTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('cdhitTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('cdhitTests.m')
+0003 function tests = cdhitTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function testCdhit(testCase)
+0008 %This unit test comprises the functionality test for CD-HIT in RAVEN:
+0009 % 1. Check for resulting file against the expected one.
+0010 
+0011 %%
+0012 %Get the directory for RAVEN Toolbox
+0013 [ST, I]=dbstack('-completenames');
+0014 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0015 
+0016 %Identify the operating system
+0017 if isunix
+0018     if ismac
+0019         binEnd='.mac';
+0020     else
+0021         binEnd='';
+0022     end
+0023 elseif ispc
+0024     binEnd='.exe';
+0025 else
+0026     dispEM('Unknown OS, exiting.')
+0027     return
+0028 end
+0029 
+0030 %Import structure that contains expected MAFFT results
+0031 sourceDir = fileparts(which(mfilename));
+0032 load([sourceDir,'/test_data/expCdhitMafftOutput.mat'],'expCdhitMafftOutput');
+0033 
+0034 %Generate temporary names for working directory and outFile
+0035 tmpDIR=tempname;
+0036 outFile=tempname;
+0037 
+0038 %Run CD-HIT multi-threaded to use all logical cores assigned to MATLAB
+0039 cores = evalc('feature(''numcores'')');
+0040 cores = strsplit(cores, 'MATLAB was assigned: ');
+0041 cores = regexp(cores{2},'^\d*','match');
+0042 cores = cores{1};
+0043 
+0044 %Create a temporary folder and copy multi-FASTA file there
+0045 [~, ~]=system(['mkdir "' tmpDIR '"']);
+0046 
+0047 sourceDir = fileparts(which(mfilename));
+0048 copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+0049 
+0050 % Define WSL paths
+0051 wslPath.fastaFile=getWSLpath([tmpDIR filesep 'yeast_galactosidases.fa']);
+0052 wslPath.outFile=getWSLpath(outFile);
+0053 wslPath.cdhit=getWSLpath(fullfile(ravenPath,'software','cd-hit','cd-hit'));
+0054 
+0055 %%
+0056 %Run protein clustering with CD-HIT
+0057 if ispc
+0058     [~, ~]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.fastaFile '" -o "' wslPath.outFile '" -c 1.0 -n 5 -M 2000']);
+0059 else
+0060     [~, ~]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" -o "' outFile '" -c 1.0 -n 5 -M 2000']);
+0061 end
+0062 
+0063 %%
+0064 %Open actual MAFFT results file
+0065 actCdhitOutput=importdata(fullfile(outFile));
+0066 
+0067 %Remove the old tempfiles
+0068 delete([outFile '*']);
+0069 
+0070 %Remove temporary folder, since testing is finished
+0071 [~, ~]=system(['rm "' tmpDIR '" -r']);
+0072 
+0073 %%
+0074 %Check 1a: Check if files for CD-HIT results are the same
+0075 verifyEqual(testCase,actCdhitOutput,expCdhitMafftOutput);
+0076 
+0077 %Check 1b: Change actual CD-HIT results file and check if test fails
+0078 actCdhitOutput='abc';
+0079 verifyNotEqual(testCase,actCdhitOutput,expCdhitMafftOutput);
+0080 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/diamondTests.html b/doc/testing/unit_tests/diamondTests.html
new file mode 100644
index 00000000..5af96de4
--- /dev/null
+++ b/doc/testing/unit_tests/diamondTests.html
@@ -0,0 +1,107 @@
+
+
+
+  Description of diamondTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > diamondTests.m
    
+
+
+
+
    diamondTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = diamondTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('diamondTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('diamondTests.m')
+0003 function tests = diamondTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function testDiamond(testCase)
+0008 %This unit test comprises several functionality tests for DIAMOND blastp in
+0009 %RAVEN:
+0010 % 1. MD5 checksum check for DIAMOND database files.
+0011 % 2. Non-parsed text check for DIAMOND result files. Although the content
+0012 %    of the files is exactly the same, their MD5 hashes are somehow
+0013 %    different between the operating systems.
+0014 % 3. Check of resulting blastStructure against the expected one. This is
+0015 %    done to test DIAMOND blastp results parsing in RAVEN.
+0016 
+0017 %%
+0018 %Get the directory for RAVEN Toolbox
+0019 [ST, I]=dbstack('-completenames');
+0020 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0021 
+0022 %Import structures that contain expected MD5 hashes and DIAMOND blastp
+0023 %results
+0024 sourceDir = fileparts(which(mfilename));
+0025 load([sourceDir,'/test_data/expDiamondResults.mat'],'expBlastStructure','expDiamondReport');
+0026 
+0027 organismID='sce';
+0028 fastaFile=fullfile(ravenPath,'testing','unit_tests','test_data','yeast_galactosidases.fa');
+0029 modelIDs={'hsa' 'afv'};
+0030 refFastaFiles={fullfile(ravenPath,'testing','unit_tests','test_data','human_galactosidases.fa') fullfile(ravenPath,'testing','unit_tests','test_data','aflavus_galactosidases.fa')};
+0031 
+0032 %%
+0033 %Run DIAMOND blastp
+0034 [actBlastStructure,actDiamondReport]=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles,true,true);
+0035 
+0036 %%
+0037 %Test 1a: Check if MD5 checksums for DIAMOND blastp database files are the same
+0038 verifyEqual(testCase,actDiamondReport.dbHashes,expDiamondReport.dbHashes);
+0039 
+0040 %Test 1b: Change one of the MD5 checksums and check if test fails
+0041 actDiamondReport.dbHashes{1,1}=actDiamondReport.dbHashes{1,2};
+0042 verifyNotEqual(testCase,actDiamondReport.dbHashes,expDiamondReport.dbHashes);
+0043 
+0044 %Test 2a: Check if DIAMOND blastp result files are the same
+0045 verifyEqual(testCase,actDiamondReport.diamondTxtOutput,expDiamondReport.diamondTxtOutput);
+0046 
+0047 %Test 2b: Change actual DIAMOND blastp result file and check if test fails
+0048 actDiamondReport.diamondTxtOutput='empty';
+0049 verifyNotEqual(testCase,actDiamondReport.diamondTxtOutput,expDiamondReport.diamondTxtOutput);
+0050 
+0051 %Test 3a: Check if DIAMOND blastp structures are the same
+0052 verifyEqual(testCase,actBlastStructure,expBlastStructure);
+0053 
+0054 %Test 3b: Modify actual DIAMOND blastp structure and check if test fails
+0055 actBlastStructure(1,1).toId=actBlastStructure(1,1).fromId;
+0056 verifyNotEqual(testCase,actBlastStructure,expBlastStructure);
+0057 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/hmmerTests.html b/doc/testing/unit_tests/hmmerTests.html
new file mode 100644
index 00000000..dec29c58
--- /dev/null
+++ b/doc/testing/unit_tests/hmmerTests.html
@@ -0,0 +1,191 @@
+
+
+
+  Description of hmmerTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > hmmerTests.m
    
+
+
+
+
    hmmerTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = hmmerTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('hmmerTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('hmmerTests.m')
+0003 function tests = hmmerTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function testHmmer(testCase)
+0008 %This unit test comprises the functionality test for HMMER in RAVEN:
+0009 % 1. Check of parsed HMMER results against the expected.
+0010 %
+0011 % NOTE: as hmm and HMMER results files are time-specific, no checks for
+0012 % these files existence are done. Also, due to the way HMMER is utilized in
+0013 % getKEGGModelForOrganism (HMMER result files can be parsed only once all
+0014 % required hmm files are generated), the code segment involving HMMER
+0015 % results parsing is pasted in this test function. Should the parsing problems
+0016 % occur in the results processing, the code modifications shall be done in
+0017 % this function and getKEGGModelForOrganism respectively.
+0018 
+0019 %%
+0020 %Get the directory for RAVEN Toolbox
+0021 [ST, I]=dbstack('-completenames');
+0022 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0023 
+0024 %Identify the operating system
+0025 if isunix
+0026     if ismac
+0027         binEnd='.mac';
+0028     else
+0029         binEnd='';
+0030     end
+0031 elseif ispc
+0032     binEnd='.exe';
+0033 else
+0034     dispEM('Unknown OS, exiting.')
+0035     return
+0036 end
+0037 
+0038 %Create empty structures needed for HMMER results
+0039 actHmmResult.genes = {};
+0040 actHmmResult.scores = [];
+0041 
+0042 %Create structures that contain expected HMMER results
+0043 expHmmResult.genes = {'sp|P41947|MEL6_YEASX','sp|P41946|MEL5_YEASX', 'sp|P41945|MEL2_YEASX', 'sp|P04824|MEL1_YEASX'};
+0044 expHmmResult.scores = [10^-250, 10^-250, 10^-250, 10^-250];
+0045 
+0046 %Generate temporary names for working directory and outFile
+0047 tmpDIR=tempname;
+0048 outFile=tempname;
+0049 
+0050 %Run HMMER multi-threaded to use all logical cores assigned to MATLAB
+0051 cores = evalc('feature(''numcores'')');
+0052 cores = strsplit(cores, 'MATLAB was assigned: ');
+0053 cores = regexp(cores{2},'^\d*','match');
+0054 cores = cores{1};
+0055 
+0056 %Create a temporary folder and copy multi-FASTA file there
+0057 [~, ~]=system(['mkdir "' tmpDIR '"']);
+0058 
+0059 sourceDir = fileparts(which(mfilename));
+0060 copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+0061 copyfile(fullfile(sourceDir,'test_data','human_galactosidases.fa'),tmpDIR);
+0062 
+0063 %%
+0064 %Train a hidden Markov model
+0065 [~, ~]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmbuild' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(tmpDIR,'human_galactosidases.hmm') '" "' fullfile(tmpDIR,'yeast_galactosidases.fa') '"']);
+0066 
+0067 %Run a homology search against the newly-trained HMM
+0068 [~, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(tmpDIR,'human_galactosidases.hmm') '" "' fullfile(tmpDIR,'yeast_galactosidases.fa') '"']);
+0069 
+0070 %Save the output to a file
+0071 fid=fopen(outFile,'w');
+0072 fwrite(fid,output);
+0073 fclose(fid);
+0074 
+0075 %%
+0076 %Parse the results
+0077 geneCounter=0;
+0078 fid=fopen(outFile,'r');
+0079 beginMatches=false;
+0080 while 1
+0081     %Get the next line
+0082     tline = fgetl(fid);
+0083     
+0084     %Abort at end of file
+0085     if ~ischar(tline)
+0086         break;
+0087     end
+0088     
+0089     if and(beginMatches,strcmp(tline,'  ------ inclusion threshold ------'))
+0090         break;
+0091     end
+0092     
+0093     if beginMatches==false
+0094         %This is how the listing of matches begins
+0095         if any(strfind(tline,'E-value '))
+0096             %Read one more line that is only padding
+0097             tline = fgetl(fid);
+0098             beginMatches=true;
+0099         end
+0100     else
+0101         %If matches should be read
+0102         if ~strcmp(tline,'   [No hits detected that satisfy reporting thresholds]') && ~isempty(tline)
+0103             elements=regexp(tline,' ','split');
+0104             elements=elements(cellfun(@any,elements));
+0105             
+0106             %Check if the match is below the treshhold
+0107             score=str2double(elements{1});
+0108             gene=elements{9};
+0109             if score<=10^-50
+0110                 %If the score is exactly 0, change it to a very
+0111                 %small value to avoid NaN
+0112                 if score==0
+0113                     score=10^-250;
+0114                 end
+0115                 %Check if the gene is added already and, is so, get
+0116                 %the best score for it
+0117                 geneCounter=geneCounter+1;
+0118                 actHmmResult.genes{geneCounter}=gene;
+0119                 actHmmResult.scores(geneCounter)=score;
+0120             end
+0121         else
+0122             break;
+0123         end
+0124     end
+0125 end
+0126 fclose(fid);
+0127 
+0128 %Remove the old tempfiles
+0129 delete([outFile '*']);
+0130 
+0131 %Remove temporary folder, since testing is finished
+0132 [~, ~]=system(['rm "' tmpDIR '" -r']);
+0133 
+0134 %%
+0135 %Test 1a: Check if HMMER results match the expected ones
+0136 verifyEqual(testCase,actHmmResult,expHmmResult);
+0137 
+0138 %Test 1b: Modify actual HMMER results structure and check if test fails
+0139 actHmmResult.score(2)=1;
+0140 verifyNotEqual(testCase,actHmmResult,expHmmResult);
+0141 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/index.html b/doc/testing/unit_tests/index.html
index 3e1a88a1..92bfb81c 100644
--- a/doc/testing/unit_tests/index.html
+++ b/doc/testing/unit_tests/index.html
@@ -19,7 +19,7 @@ 
    Index for testing\unit_tests
    
 
 
    Matlab files in this directory:
    
 
-
     tinitTestsrun this test case with the command 
    
+ blastPlusTestsrun this test case with the command  cdhitTestsrun this test case with the command  diamondTestsrun this test case with the command  hmmerTestsrun this test case with the command  mafftTestsrun this test case with the command  sortIdentifiers_and_permuteModelTestsrun this test case with the command  tinitTestsrun this test case with the command 
 
 
 
    Subsequent directories:
    
diff --git a/doc/testing/unit_tests/mafftTests.html b/doc/testing/unit_tests/mafftTests.html
new file mode 100644
index 00000000..4a31ad61
--- /dev/null
+++ b/doc/testing/unit_tests/mafftTests.html
@@ -0,0 +1,118 @@
+
+
+
+  Description of mafftTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > mafftTests.m
    
+
+
+
+
    mafftTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = mafftTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('mafftTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('mafftTests.m')
+0003 function tests = mafftTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function testMafft(testCase)
+0008 %This unit test comprises the functionality test for MAFFT in RAVEN:
+0009 % 1. Check for resulting file against the expected one.
+0010 
+0011 %%
+0012 %Get the directory for RAVEN Toolbox
+0013 [ST, I]=dbstack('-completenames');
+0014 ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+0015 
+0016 %Import structure that contains expected MAFFT results
+0017 sourceDir = fileparts(which(mfilename));
+0018 load([sourceDir,'/test_data/expCdhitMafftOutput.mat'],'expCdhitMafftOutput');
+0019 
+0020 %Generate temporary names for working directory and outFile
+0021 tmpDIR=tempname;
+0022 outFile=tempname;
+0023 
+0024 %Run MAFFT multi-threaded to use all logical cores assigned to MATLAB
+0025 cores = evalc('feature(''numcores'')');
+0026 cores = strsplit(cores, 'MATLAB was assigned: ');
+0027 cores = regexp(cores{2},'^\d*','match');
+0028 cores = cores{1};
+0029 
+0030 %Create a temporary folder and copy multi-FASTA file there
+0031 [~, ~]=system(['mkdir "' tmpDIR '"']);
+0032 
+0033 sourceDir = fileparts(which(mfilename));
+0034 copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+0035 
+0036 % Define WSL paths
+0037 wslPath.fastaFile=getWSLpath([tmpDIR filesep 'yeast_galactosidases.fa']);
+0038 wslPath.outFile=getWSLpath(outFile);
+0039 wslPath.mafft=getWSLpath(fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat'));
+0040 
+0041 %%
+0042 %Run protein multi-sequence alignment with MAFFT
+0043 if ismac
+0044     [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-mac','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
+0045 elseif isunix
+0046     [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
+0047 elseif ispc
+0048     [~, ~]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --quiet --thread "' num2str(cores) '" --out "' wslPath.outFile '" "' wslPath.fastaFile '"']);
+0049 end
+0050 
+0051 %%
+0052 %Open actual MAFFT results file
+0053 actMafftOutput=importdata(fullfile(outFile));
+0054 
+0055 %Remove the old tempfiles
+0056 delete([outFile '*']);
+0057 
+0058 %Remove temporary folder, since testing is finished
+0059 [~, ~]=system(['rm "' tmpDIR '" -r']);
+0060 
+0061 %%
+0062 %Check 1a: Check if files for MAFFT results are the same
+0063 verifyEqual(testCase,actMafftOutput,expCdhitMafftOutput);
+0064 
+0065 %Check 1b: Change actual MAFFT results file and check if test fails
+0066 actMafftOutput='abc';
+0067 verifyNotEqual(testCase,actMafftOutput,expCdhitMafftOutput);
+0068 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html b/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html
new file mode 100644
index 00000000..7584e7e1
--- /dev/null
+++ b/doc/testing/unit_tests/sortIdentifiers_and_permuteModelTests.html
@@ -0,0 +1,104 @@
+
+
+
+  Description of sortIdentifiers_and_permuteModelTests
+  
+  
+  
+  
+  
+  
+
+
+
+
    Home >  testing > unit_tests > sortIdentifiers_and_permuteModelTests.m
    
+
+
+
+
    sortIdentifiers_and_permuteModelTests
+
    
+
+
    PURPOSE ^
    
+
    run this test case with the command
    
+
+
    SYNOPSIS ^
    
+
    function tests = sortIdentifiers_and_permuteModelTests 
    
+
+
    DESCRIPTION ^
    
+
    run this test case with the command
+results = runtests('sortIdentifiers_and_permuteModelTests.m')
    
+
+
+
    CROSS-REFERENCE INFORMATION ^
    
+This function calls:
+
+This function is called by:
+
+
+
+
    SUBFUNCTIONS ^
    
+
+
+
    SOURCE CODE ^
    
+
    0001 %run this test case with the command
+0002 %results = runtests('sortIdentifiers_and_permuteModelTests.m')
+0003 function tests = sortIdentifiers_and_permuteModelTests
+0004 tests = functiontests(localfunctions);
+0005 end
+0006 
+0007 function sortRandomizedModelTest(testCase)
+0008 
+0009 %Load the expected (i.e. sorted) model
+0010 sourceDir = fileparts(which(mfilename));
+0011 load([sourceDir,'/test_data/ecoli_textbook.mat'], 'model');
+0012 expModel = model;
+0013 
+0014 %Create the actual model that will be permuted and sorted
+0015 actModel = expModel;
+0016 
+0017 %Randomly permutate model, do not use RAVEN functions
+0018 rndIdx = randperm(numel(actModel.rxns));
+0019 fieldsToChange = {'rxns','lb','ub','rev','c','rxnNames','grRules','eccodes'};
+0020 for i=1:numel(fieldsToChange)
+0021     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0022 end
+0023 actModel.S          = actModel.S(:,rndIdx);
+0024 actModel.rxnGeneMat = actModel.rxnGeneMat(rndIdx,:);
+0025 
+0026 rndIdx = randperm(numel(actModel.mets));
+0027 fieldsToChange = {'mets','metNames','metComps','metFormulas'};
+0028 for i=1:numel(fieldsToChange)
+0029     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0030 end
+0031 actModel.S     = actModel.S(rndIdx,:);
+0032 
+0033 rndIdx = randperm(numel(actModel.genes));
+0034 fieldsToChange = {'genes','geneShortNames'};
+0035 for i=1:numel(fieldsToChange)
+0036     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0037 end
+0038 actModel.rxnGeneMat = actModel.rxnGeneMat(:,rndIdx);
+0039 
+0040 rndIdx = randperm(numel(actModel.comps));
+0041 fieldsToChange = {'comps','compNames'};
+0042 for i=1:numel(fieldsToChange)
+0043     actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+0044 end
+0045 [~,J]=sort(rndIdx);
+0046 [toreplace, bywhat] = ismember(actModel.metComps,1:length(J));
+0047 actModel.metComps(toreplace) = J(bywhat(toreplace));
+0048 
+0049 %Sort randomly permutated model
+0050 actModel = sortIdentifiers(actModel);
+0051 
+0052 %Check that the actual model is the same as the expected model
+0053 verifyEqual(testCase,actModel,expModel)
+0054 end
    
+
    Generated by m2html © 2005
    
+
+
\ No newline at end of file
diff --git a/doc/testing/unit_tests/tinitTests.html b/doc/testing/unit_tests/tinitTests.html
index 2ad5a268..247f542f 100644
--- a/doc/testing/unit_tests/tinitTests.html
+++ b/doc/testing/unit_tests/tinitTests.html
@@ -12,7 +12,7 @@
 
 
 
-
    Home >  testing > unit_tests > tinitTests.m
    
+
    Home >  testing > unit_tests > tinitTests.m
    
 
 
diff --git a/doc/tutorial/tutorial5.html b/doc/tutorial/tutorial5.html
index 177ff49e..6aa64dc0 100644
--- a/doc/tutorial/tutorial5.html
+++ b/doc/tutorial/tutorial5.html
@@ -70,10 +70,10 @@ 
    SOURCE CODE ^%are for. This process takes up to 20-35 minutes in macOS, Unix systems and
 0020 %40-55 minutes in Windows, depending on your hardware and the size of
 0021 %target organism proteome
-0022 model=getKEGGModelForOrganism('sce','sce.fa','euk100_kegg94','output',false,false,false,false,10^-30,0.8,0.3,-1);
+0022 model=getKEGGModelForOrganism('sce','sce.fa','euk90_kegg100','output',false,false,false,false,10^-30,0.8,0.3,-1);
 0023 
-0024 %The resulting model should contain around 1669 reactions, 1677
-0025 %metabolites and 838 genes. Small variations are possible since it is an
+0024 %The resulting model should contain around 1590 reactions, 1571
+0025 %metabolites and 837 genes. Small variations are possible since it is an
 0026 %heuristic algorithm and different KEGG versions will give slightly
 0027 %different results.
 0028 disp(model);
diff --git a/external/getBlast.m b/external/getBlast.m
index 44e3d11f..f9567527 100755
--- a/external/getBlast.m
+++ b/external/getBlast.m
@@ -1,7 +1,8 @@
-function blastStructure=getBlast(organismID,fastaFile,modelIDs,refFastaFiles)
+function [blastStructure,blastReport]=getBlast(organismID,fastaFile,...
+    modelIDs,refFastaFiles,develMode,hideVerbose)
 % getBlast
-%   Performs a bidirectional BLASTP between the organism of interest and a
-%   set of template organisms.
+%   Performs a bidirectional BLAST between the organism of interest and a
+%   set of template organisms
 %
 %   Input:
 %   organismID      the id of the organism of interest. This should also
@@ -13,19 +14,34 @@
 %                   output is to be used with getModelFromHomology
 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
 %                   files
-%   
-%   Output: 
+%   develMode       true if blastReport should be generated that is used
+%                   in the unit testing function for BLAST+ (opt, default
+%                   false)
+%   hideVerbose     true if no status messages should be printed (opt,
+%                   default false)
+%
+%   Output:
 %   blastStructure  structure containing the bidirectional homology
-%                   measurements which are used by getModelFromHomology
+%                   measurements that can be used by getModelFromHomology
+%   blastReport     structure containing MD5 hashes for FASTA database
+%                   files and non-parsed BLAST output data. Will be blank
+%                   if develMode is false.
 %
-%   NOTE: This function calls BLASTP to perform a bidirectional homology
+%   NOTE: This function calls BLAST+ to perform a bidirectional homology
 %   test between the organism of interest and a set of other organisms
-%   using standard settings. The only filtering this functions does is the
-%   removal of hits with E value higher than 10e-5. If you would like to
-%   use other homology measurements, please see getBlastFromExcel.
+%   using standard settings. The only filtering this function does is the
+%   removal of hits with an E-value higher than 10e-5. The other homology
+%   measurements can be implemented using getBlastFromExcel.
 %
-%   Usage: blastStructure=getBlast(organismID,fastaFile,modelIDs,...
-%           refFastaFiles)
+%   Usage: [blastStructure,blastReport]=getBlast(organismID,fastaFile,...
+%    modelIDs,refFastaFiles,develMode,hideVerbose)
+
+if nargin<5
+    develMode = false;
+end
+if nargin<6
+    hideVerbose = false;
+end
 
 %Everything should be cell arrays
 organismID=cellstr(organismID);
@@ -33,14 +49,20 @@
 modelIDs=cellstr(modelIDs);
 refFastaFiles=cellstr(refFastaFiles);
 
+%Create blank structures for results
 blastStructure=[];
+blastReport.dbHashes.phr={};
+blastReport.dbHashes.pot={};
+blastReport.dbHashes.psq={};
+blastReport.dbHashes.pto={};
+blastReport.blastTxtOutput={};
 
 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
 %way to do this
 [ST, I]=dbstack('-completenames');
 ravenPath=fileparts(fileparts(ST(I).file));
 
-%Construct databases and output file
+%Generate temporary names for BLAST databases and output files
 tmpDB=tempname;
 outFile=tempname;
 
@@ -52,12 +74,11 @@
     files=vertcat(fastaFile,refFastaFiles);
 end
 
-files=checkFileExistence(files,true,false); %No whitespace allowed
+files=checkFileExistence(files,2); %Copy files to temp dir
 fastaFile = files(1);
 refFastaFiles = files(2:end);
 
-%Create a database for the new organism and blast each of the refFastaFiles
-%against it
+%Identify the operating system
 if isunix
     if ismac
         binEnd='.mac';
@@ -65,50 +86,72 @@
         binEnd='';
     end
 elseif ispc
-    binEnd='';
+    binEnd='.exe';
     setenv('BLASTDB_LMDB_MAP_SIZE','1000000');
 else
     dispEM('Unknown OS, exiting.')
     return
 end
 
-% Run BLAST multi-threaded to use all logical cores assigned to MATLAB.
+%Run BLAST multi-threaded to use all logical cores assigned to MATLAB
 cores = evalc('feature(''numcores'')');
 cores = strsplit(cores, 'MATLAB was assigned: ');
 cores = regexp(cores{2},'^\d*','match');
 cores = cores{1};
 
-[status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' fastaFile{1} '" -out "' tmpDB '" -dbtype prot']);
+%Create a database for the new organism and blast each of the refFastaFiles
+%against it
+[status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in ' fastaFile{1} ' -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']);
+if develMode
+    blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.phr'));
+    blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pot'));
+    blastReport.dbHashes.psq{numel(blastReport.dbHashes.psq)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.psq'));
+    blastReport.dbHashes.pto{numel(blastReport.dbHashes.pto)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pto'));
+end
 if status~=0
     EM=['makeblastdb did not run successfully, error: ', num2str(status)];
     dispEM(EM,true);
 end
 
 for i=1:numel(refFastaFiles)
-    fprintf(['BLASTing "' modelIDs{i} '" against "' organismID{1} '"..\n']);
-    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' refFastaFiles{i} '" -out "' outFile '_' num2str(i) '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
+    if ~hideVerbose
+        fprintf(['BLASTing "' modelIDs{i} '" against "' organismID{1} '"..\n']);
+    end
+    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query ' refFastaFiles{i} ' -out "' outFile '_' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
+    if develMode
+        blastReport.blastTxtOutput{numel(blastReport.blastTxtOutput)+1}=importdata([outFile '_' num2str(i)]);
+    end
     if status~=0
         EM=['blastp did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
 end
-delete([tmpDB '*']);
+delete([tmpDB filesep 'tmpDB*']);
 
 %Then create a database for each of the reference organisms and blast the
 %new organism against them
 for i=1:numel(refFastaFiles)
-    fprintf(['BLASTing "' organismID{1} '" against "' modelIDs{i} '"..\n']);
-    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' refFastaFiles{i} '" -out "' tmpDB '" -dbtype prot']);
+    if ~hideVerbose
+        fprintf(['BLASTing "' organismID{1} '" against "' modelIDs{i} '"..\n']);
+    end
+    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in ' refFastaFiles{i} ' -out "' fullfile(tmpDB, 'tmpDB') '" -dbtype prot']);
     if status~=0
         EM=['makeblastdb did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
-    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' fastaFile{1} '" -out "' outFile '_r' num2str(i) '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
-    delete([tmpDB '*']);
+    [status, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query ' fastaFile{1} ' -out "' outFile '_r' num2str(i) '" -db "' fullfile(tmpDB, 'tmpDB') '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
+    if develMode
+        blastReport.dbHashes.phr{numel(blastReport.dbHashes.phr)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.phr'));
+        blastReport.dbHashes.pot{numel(blastReport.dbHashes.pot)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pot'));
+        blastReport.dbHashes.psq{numel(blastReport.dbHashes.psq)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.psq'));
+        blastReport.dbHashes.pto{numel(blastReport.dbHashes.pto)+1}=getMD5Hash(fullfile(tmpDB, 'tmpDB.pto'));
+        blastReport.blastTxtOutput{numel(blastReport.blastTxtOutput)+1}=importdata([outFile '_r' num2str(i)]);
+    end    
     if status~=0
         EM=['blastp did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
+    delete([tmpDB filesep 'tmpDB*']);
 end
 
 %Done with the BLAST, do the parsing of the text files
@@ -135,4 +178,6 @@
 
 %Remove the old tempfiles
 delete([outFile '*']);
+%Remove the temp fasta files
+delete(files{:})
 end
diff --git a/external/getDiamond.m b/external/getDiamond.m
index 57820799..92018543 100755
--- a/external/getDiamond.m
+++ b/external/getDiamond.m
@@ -1,7 +1,8 @@
-function blastStructure=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles)
+function [blastStructure,diamondReport]=getDiamond(organismID,fastaFile,...
+    modelIDs,refFastaFiles,develMode,hideVerbose)
 % getDiamond
-%   Uses DIAMOND to performs a bidirectional BLASTP between the organism
-%   of interest and a set of template organisms.
+%   Uses DIAMOND to perform a bidirectional BLAST between the organism
+%   of interest and a set of template organisms
 %
 %   Input:
 %   organismID      the id of the organism of interest. This should also
@@ -13,20 +14,35 @@
 %                   output is to be used with getModelFromHomology
 %   refFastaFiles   a cell array with the paths to the corresponding FASTA
 %                   files
+%   develMode       true if blastReport should be generated that is used
+%                   in the unit testing function for DIAMOND (opt, default
+%                   false)
+%   hideVerbose     true if no status messages should be printed (opt,
+%                   default false)
 %
 %   Output:
 %   blastStructure  structure containing the bidirectional homology
 %                   measurements which are used by getModelFromHomology
+%   diamondReport   structure containing MD5 hashes for FASTA database
+%                   files and non-parsed BLAST output data. Will be blank
+%                   if develMode is false.
 %
 %   NOTE: This function calls DIAMOND to perform a bidirectional homology
-%   test between the organism of interest and a set of other organisms
+%   search between the organism of interest and a set of other organisms
 %   using the '--more-sensitive' setting from DIAMOND. For the most
 %   sensitive results, the use of getBlast() is adviced, however,
 %   getDiamond() is a fast alternative (>15x faster). The blastStructure
 %   generated is in the same format as those obtained from getBlast().
 %
-%   Usage: blastStructure=getDiamond(organismID,fastaFile,modelIDs,...
-%           refFastaFiles)
+%   Usage: [blastStructure,diamondReport]=getDiamond(organismID,fastaFile,...
+%    modelIDs,refFastaFiles,develMode,hideVerbose)
+
+if nargin<5
+    develMode = false;
+end
+if nargin<6
+    hideVerbose = false;
+end
 
 %Everything should be cell arrays
 organismID=cellstr(organismID);
@@ -34,14 +50,17 @@
 modelIDs=cellstr(modelIDs);
 refFastaFiles=cellstr(refFastaFiles);
 
+%Create blank structures for results
 blastStructure=[];
+diamondReport.dbHashes={};
+diamondReport.diamondTxtOutput={};
 
 %Get the directory for RAVEN Toolbox. This may not be the easiest or best
 %way to do this
 [ST, I]=dbstack('-completenames');
 ravenPath=fileparts(fileparts(ST(I).file));
 
-%Construct databases and output file
+%Generate temporary names for DIAMOND databases and output files
 tmpDB=tempname;
 outFile=tempname;
 
@@ -53,13 +72,11 @@
     files=vertcat(fastaFile,refFastaFiles);
 end
 
-files=checkFileExistence(files,true,false); %No whitespace allowed
+files=checkFileExistence(files,2); %Copy files to temp dir
 fastaFile = files(1);
 refFastaFiles = files(2:end);
 
-%Create a database for the new organism and blast each of the refFastaFiles
-%against it
-
+%Identify the operating system
 if isunix
     if ismac
         binEnd='.mac';
@@ -67,49 +84,65 @@
         binEnd='';
     end
 elseif ispc
-    binEnd='';
+    binEnd='.exe';
 else
     dispEM('Unknown OS, exiting.')
     return
 end
 
-% Run BLAST multi-threaded to use all logical cores assigned to MATLAB.
+%Run DIAMOND multi-threaded to use all logical cores assigned to MATLAB.
 cores = evalc('feature(''numcores'')');
 cores = strsplit(cores, 'MATLAB was assigned: ');
 cores = regexp(cores{2},'^\d*','match');
 cores = cores{1};
 
-[status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' tmpDB '"']);
+%Create a database for the new organism and blast each of the refFastaFiles
+%against it
+[status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fastaFile{1} '" --db "' fullfile(tmpDB) '"']);
+if develMode
+    diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message,'[a-f0-9]{32}','match'));
+end
 if status~=0
     EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
     dispEM(EM,true);
 end
 
 for i=1:numel(refFastaFiles)
-    fprintf(['Running DIAMOND blastp with "' modelIDs{i} '" against "' organismID{1} '"..\n']);
-    [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
+    if ~hideVerbose
+        fprintf(['Running DIAMOND blastp with "' modelIDs{i} '" against "' organismID{1} '"..\n']);
+    end
+    [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' refFastaFiles{i} '" --out "' outFile '_' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
+    if develMode
+        diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_' num2str(i)]);
+    end
     if status~=0
         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
 end
-delete([tmpDB '*']);
+delete([tmpDB filesep 'tmpDB*']);
 
 %Then create a database for each of the reference organisms and blast the
 %new organism against them
 for i=1:numel(refFastaFiles)
-    fprintf(['Running DIAMOND blastp with "' organismID{1} '" against "' modelIDs{i} '"..\n']);
-    [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' tmpDB '"']);
+    if ~hideVerbose
+        fprintf(['Running DIAMOND blastp with "' organismID{1} '" against "' modelIDs{i} '"..\n']);
+    end
+    [status, message]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' refFastaFiles{i} '" --db "' fullfile(tmpDB) '"']);
     if status~=0
         EM=['DIAMOND makedb did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
-    [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]);
-    delete([tmpDB '*']);
+    [status, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fastaFile{1} '" --out "' outFile '_r' num2str(i) '" --db "' fullfile(tmpDB) '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores]);
+    if develMode
+        diamondReport.dbHashes{numel(diamondReport.dbHashes)+1} = char(regexp(message,'[a-f0-9]{32}','match'));
+        diamondReport.diamondTxtOutput{numel(diamondReport.diamondTxtOutput)+1}=importdata([outFile '_r' num2str(i)]);
+    end
     if status~=0
         EM=['DIAMOND blastp did not run successfully, error: ', num2str(status)];
         dispEM(EM,true);
     end
+    delete([tmpDB filesep 'tmpDB*']);
 end
 
 %Done with the DIAMOND blastp, do the parsing of the text files
@@ -136,4 +169,6 @@
 
 %Remove the old tempfiles
 delete([outFile '*']);
+%Remove the temp fasta files
+delete(files{:})
 end
diff --git a/external/kegg/constructMultiFasta.m b/external/kegg/constructMultiFasta.m
index 83e97663..daaec2aa 100755
--- a/external/kegg/constructMultiFasta.m
+++ b/external/kegg/constructMultiFasta.m
@@ -90,11 +90,10 @@ function constructMultiFasta(model,sourceFile,outputDir)
         end
     end
 end
-fprintf('COMPLETE\n');
+fprintf('COMPLETE\n');    
 
-fprintf('Generating the KEGG Orthology specific multi-FASTA files... ');
+fprintf('Generating the KEGG Orthology specific multi-FASTA files...   0%% complete');
 %Loop through the reactions and print the corresponding sequences
-progressFlag=0;
 for i=1:numel(model.rxns)
 
     %Do not overwrite existing files
@@ -141,17 +140,14 @@ function constructMultiFasta(model,sourceFile,outputDir)
         end
         fclose(rxnfid);
     end
-    %Print the progress: no need to update this for every
-    %iteration, just report once 25%, 50% and 75% are done
-    if progressFlag==0 && i>numel(model.rxns)*0.25
-        fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(outputDir,'*.fa')))/numel(model.rxns))*100);
-        progressFlag=progressFlag+1;
-    elseif (progressFlag==1 && i>=numel(model.rxns)*0.5) || (progressFlag==2 && i>=numel(model.rxns)*0.75)
-        fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(outputDir,'*.fa')))/numel(model.rxns))*100);
-        progressFlag=progressFlag+1;
+    %Print the progress
+    if rem(i-1,50) == 0
+        progress=num2str(i/numel(model.rxns));
+        progress=pad(progress,3,'left');
+        fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
     end
 end
-fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
 
 %Close the source file
 fclose(fid);
diff --git a/external/kegg/getKEGGModelForOrganism.m b/external/kegg/getKEGGModelForOrganism.m
index 8d4fd8c6..efdaed86 100755
--- a/external/kegg/getKEGGModelForOrganism.m
+++ b/external/kegg/getKEGGModelForOrganism.m
@@ -1,7 +1,7 @@
 function model=getKEGGModelForOrganism(organismID,fastaFile,dataDir,...
     outDir,keepSpontaneous,keepUndefinedStoich,keepIncomplete,...
     keepGeneral,cutOff,minScoreRatioKO,minScoreRatioG,maxPhylDist,...
-    nSequences,seqIdentity)
+    nSequences,seqIdentity,globalModel)
 % getKEGGModelForOrganism
 %   Reconstructs a genome-scale metabolic model based on protein homology
 %   to the orthologies in KEGG. If the target species is not available in
@@ -42,7 +42,7 @@
 %                       the HMMs were trained on pro- or eukaryotic
 %                       sequences, using a sequence similarity threshold of
 %                       XXX %, fitting the KEGG version YY. E.g.
-%                       euk100_kegg82. (opt, see note about fastaFile. Note
+%                       euk90_kegg100. (opt, see note about fastaFile. Note
 %                       that in order to rebuild the KEGG model from a
 %                       database dump, as opposed to using the version
 %                       supplied with RAVEN, you would still need to supply
@@ -99,10 +99,16 @@
 %                       running CD-HIT (opt, default inf)
 %   seqIdentity         sequence identity threshold in CD-HIT, referred as
 %                       "global sequence identity" in CD-HIT User's Guide.
-%                       The only possible options are 1 (100 %), 0.9 (90 %)
-%                       and 0.5 (50 %). If other values are provided,
-%                       CD-HIT is skipped (opt, default -1, i.e. CD-HIT is
-%                       skipped)
+%                       If -1 is provided, CD-HIT is skipped (opt, default 0.9)
+%   globalModel         structure containing both model and KOModel
+%                       structures as generated by getModelFromKEGG. These
+%                       will otherwise be loaded by via getModelFromKEGG. 
+%                       Providing globalKEGGmodel can speed up model
+%                       generation if getKEGGModelForOrganism is run
+%                       multiple times for different strains. Example:
+%                       [globalModel.model,globalModel.KOModel] = getModelFromKEGG;
+%                       (opt, default empty, global model is loaded by 
+%                       getModelFromKEGG)
 %
 %   Output:
 %   model               the reconstructed model
@@ -144,30 +150,8 @@
 %   2b. KO-specific protein FASTA files are re-organised into
 %       non-redundant protein sets with CD-HIT. The user can only set
 %       seqIdentity parameter, which corresponds to '-c' parameter in
-%       CD-HIT, described as "sequence identity threshold". The following
-%       non-default parameter settings are used depending on seqIdentity
-%       value:
-%       __________________________________________________________________
-%       |                           |         seqIdentity value          |
-%       |                           --------------------------------------
-%       |                           |  1.0   |  0.9   |  0.5   |    x    |
-%       | CD-HIT parameters         -------------------------------------|
-%       -----------------------------------------------------------------|
-%       | Input Dataset (-i)        | raw    | cdh100 | cdh90  | raw     |
-%       | Output Dataset (-o)       | cdh100 | cdh90  | cdh50  | cdhOth  |
-%       | Sequence identity (-c)    | 1.0    | 0.9    | 0.5    | x       |
-%       | word_length (-n)          | 5      | 5      | 4      | 2-5*    |
-%       | Max available memory (-M) |               2000                 |
-%       ------------------------------------------------------------------        
-%       * - word length depends from sequence identity value (see CD-HIT
-%       manual for more details)
-%
-%       The table reads as follows: if seqIdentity is equal to 1, then
-%       "cdh100" set is produced from raw set of proteins. If seqIdentity
-%       is equal to 0.9, then "cdh90" is produced from "cdh100" proteins
-%       set. When seqIdentity is equal to 0.5, "cdh50" is obtained from
-%       "cdh90" protein set. Finally, if other seqIdentity value is used,
-%       it is obtained directly from the raw set of proteins.
+%       CD-HIT, described as "sequence identity threshold". CD-HIT suggsted
+%       sequence identity specific word_length (-n) parameters are used.
 %   2c. Does a multi sequence alignment for multi-FASTA files obtained in
 %       Step 2b for future use. MAFFT software with automatic selection of
 %       alignment algorithm is used in this step ('--auto').
@@ -311,8 +295,7 @@
     %Include all sequences for each reaction
 end
 if nargin<14
-    seqIdentity=-1;
-    %CD-HIT is not used in the pipeline
+    seqIdentity=0.9;
 end
 
 if isempty(fastaFile)
@@ -320,7 +303,7 @@
 else
     fprintf('\n\n*** The model reconstruction from KEGG based on the protein homology search against KEGG Orthology specific HMMs ***\n\n');
     %Check if query fasta exists
-    fastaFile=checkFileExistence(fastaFile,true,false);
+    fastaFile=checkFileExistence(fastaFile,2); %Copy file to temp dir
 end
 
 %Run the external binaries multi-threaded to use all logical cores assigned
@@ -340,27 +323,14 @@
 %required zip file already in working directory or have it extracted. If
 %the zip file and directory is not here, it is downloaded from the cloud
 if ~isempty(dataDir)
-    hmmOptions={'euk100_kegg94', ...
-        'euk90_kegg94', ...
-        'euk50_kegg94', ...
-        'prok100_kegg94', ...
-        'prok90_kegg94', ...
-        'prok50_kegg94'};
-    hmmLinks={'wbnghgtpgftb6pcw572bhkl9a8ekh32d', ...
-        '754bdz0965261fktzlwc77rcv7me87i6', ...
-        '5xwgv17cn099xn7bxo2dq5h1dsdxrhn7', ...
-        'azpn5lwrb4gind2mn5hnbmux0lao5vt5', ...
-        'j19ybilr7js34uisnss92gvq5g6lljkk', ...
-        'b5vn631jrwdzcj4uwmvbshe2ws3zoalm'};
-    if all(cellfun(@isempty,regexp(dataDir,strcat(hmmOptions,'$')))) %Check if dataDir ends with any of the hmmOptions
+    hmmOptions={'euk90_kegg100','prok90_kegg100'};
+    if ~endsWith(dataDir,hmmOptions) %Check if dataDir ends with any of the hmmOptions.
+                                     %If not, then check whether the required folders exist anyway.
         if ~exist(fullfile(dataDir,'keggdb','genes.pep'),'file') && ...
                 ~exist(fullfile(dataDir,'fasta'),'dir') && ...
                 ~exist(fullfile(dataDir,'aligned'),'dir') && ...
                 ~exist(fullfile(dataDir,'hmms'),'dir')
-            EM='Pre-trained HMMs set is not recognised. It should match any of the following sets:';
-            disp(EM);
-            disp(hmmOptions);
-            error('Fatal error occured. See the details above');
+            error(['Pre-trained HMMs set is not recognised. If you want download RAVEN provided sets, it should match any of the following: ' strjoin(hmmOptions,' or ')])
         end
     else
         if exist(dataDir,'dir') && exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
@@ -370,14 +340,18 @@
             unzip([dataDir,'.zip']);
             fprintf('COMPLETE\n');
         else
-            hmmIndex=regexp(dataDir,hmmOptions);
-            hmmIndex=~cellfun(@isempty,hmmIndex);
-            fprintf('Downloading the HMMs archive file... ');
-            try
-                websave([dataDir,'.zip'],['https://chalmersuniversity.box.com/shared/static/',hmmLinks{hmmIndex},'.zip']);
-            catch ME
-                if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
-                    error('Failed to download the HMMs archive file, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues')
+            hmmIndex=strcmp(dataDir,hmmOptions);
+            if ~any(hmmIndex)
+                error(['Pre-trained HMMs are only provided with proteins clustered at 90% sequence identity (i.e. prok90_kegg100 and euk90_kegg100). ' ...
+                    'Use either of these datasets, or otherwise download the relevant sequence data from KEGG to train HMMs with your desired sequence identity'])
+            else
+                fprintf('Downloading the HMMs archive file... ');
+                try
+                    websave([dataDir,'.zip'],['https://github.com/SysBioChalmers/RAVEN/releases/download/v2.6.0/',hmmOptions{hmmIndex},'.zip']);
+                catch ME
+                    if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
+                        error('Failed to download the HMMs archive file, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues')
+                    end
                 end
             end
             
@@ -388,9 +362,7 @@
         end
         %Check if HMMs are extracted
         if ~exist(fullfile(dataDir,'hmms','K00844.hmm'),'file')
-            EM=['The HMM files seem improperly extracted and not found in ',dataDir,'/hmms. Please remove ',dataDir,' folder and rerun getKEGGModelForOrganism'];
-            disp(EM);
-            error('Fatal error occured. See the details above');
+            error(['The HMM files seem improperly extracted and not found in ',dataDir,'/hmms. Please remove ',dataDir,' folder and rerun getKEGGModelForOrganism']);
         end
     end
 end
@@ -419,9 +391,13 @@
     end
 end
 
-%First generate the full KEGG model. The dataDir must not be supplied as
+%First generate the full global KEGG model. Can be provided as input.
+%Otherwise, getModelFromKEGG is run. The dataDir must not be supplied as
 %there is also an internal RAVEN version available
-if any(dataDir)
+if nargin==15
+    model=globalModel.model;
+    KOModel=globalModel.KOModel;
+elseif any(dataDir)
     [model, KOModel]=getModelFromKEGG(fullfile(dataDir,'keggdb'),keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
 else
     [model, KOModel]=getModelFromKEGG([],keepSpontaneous,keepUndefinedStoich,keepIncomplete,keepGeneral);
@@ -432,6 +408,13 @@
 %If no FASTA file is supplied, then just remove all genes which are not for
 %the given organism ID
 if isempty(fastaFile)
+    %Check if organismID can be found in KEGG species list or is
+    %set to "eukaryotes" or "prokaryotes"
+    phylDistsFull=getPhylDist(fullfile(dataDir,'keggdb'),true);
+    if ~ismember(organismID,[phylDistsFull.ids 'eukaryotes' 'prokaryotes'])
+        error('Provided organismID is incorrect. Only species abbreviations from KEGG Species List or "eukaryotes"/"prokaryotes" are allowed.');
+    end
+    
     fprintf(['Pruning the model from non-' organismID ' genes... ']);
     if ismember(organismID,{'eukaryotes','prokaryotes'})
         phylDists=getPhylDist(fullfile(dataDir,'keggdb'),maxPhylDist==-1);
@@ -477,15 +460,8 @@
 
 %Clean gene names
 fprintf('Fixing gene names in the model... ');
-for i=1:numel(model.genes)
-    %First get rid of the prefix organism id
-    model.genes{i}=model.genes{i}(strfind(model.genes{i},':')+1:end);
-    %Find and remove the description in parentheses if any
-    s=strfind(model.genes{i},'(');
-    if any(s)
-        model.genes{i}=model.genes{i}(1:s-1);
-    end
-end
+%Get rid of the prefix organism id
+model.genes=regexprep(model.genes,'^\w+?:','');
 fprintf('COMPLETE\n');
 
 %If no FASTA file is supplied, then we are done here
@@ -588,16 +564,23 @@
 missingAligned=setdiff(KOModel.rxns,[alignedFiles;hmmFiles;alignedWorking;outFiles]);
 if ~isempty(missingAligned)
     if seqIdentity==-1
-        fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets... ');
+        fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets...   0%% complete');
     else
-        fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets... ');
+        fprintf('Performing clustering and multiple alignment for KEGG Orthology specific protein sets...   0%% complete');
     end
     missingAligned=missingAligned(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingAligned)));
-    progressFlag=0;
-    %Update fastaFiles. This is needed once rebuilding KEGG from FTP dump
-    %files for more accurate progress reporting
-    fastaFiles=listFiles(fullfile(dataDir,'fasta','*.fa'));
-    %Align all sequences using MAFFT
+    tmpFile=tempname;
+    %On Windows, paths need to be translated to Unix before parsing it to WSL
+    if ispc
+        wslPath.tmpFile=getWSLpath(tmpFile);
+        %mafft has problems writing to terminal (/dev/stderr) when running
+        %on WSL via MATLAB, instead write and read progress file
+        mafftOutput = tempname;
+        wslPath.mafftOutput=getWSLpath(mafftOutput);
+        wslPath.mafft=getWSLpath(fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat'));
+        wslPath.cdhit=getWSLpath(fullfile(ravenPath,'software','cd-hit','cd-hit'));
+    end
+    
     for i=1:numel(missingAligned)
         %This is checked here because it could be that it is created by a
         %parallel process. The faw-files are saved as temporary files to
@@ -662,78 +645,27 @@
             %Do the clustering and alignment if there are more than one
             %sequences, otherwise just save the sequence (or an empty file)
             if numel(fastaStruct)>1
-                if seqIdentity==0.9
-                    cdhitInp100=tempname;
-                    fastawrite(cdhitInp100,fastaStruct);
-                    cdhitInp90=tempname;
-                    [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
-                    if status~=0
-                        EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-                        dispEM(EM);
-                    end
-                    %Remove the old tempfile
-                    if exist(cdhitInp100, 'file')
-                        delete([cdhitInp100 '*']);
-                    end
-                    tmpFile=tempname;
-                    [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' tmpFile '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
-                    if status~=0
-                        EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-                        dispEM(EM);
-                    end
-                    %Remove the old tempfile
-                    if exist(cdhitInp90, 'file')
-                        delete([cdhitInp90 '*']);
-                    end
-                elseif seqIdentity==0.5
-                    cdhitInp100=tempname;
-                    fastawrite(cdhitInp100,fastaStruct);
-                    cdhitInp90=tempname;
-                    [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp100 '" -o "' cdhitInp90 '" -c 1.0 -n 5 -M 2000']);
-                    if status~=0
-                        EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-                        dispEM(EM);
-                    end
-                    %Remove the old tempfile
-                    if exist(cdhitInp100, 'file')
-                        delete([cdhitInp100 '*']);
-                    end
-                    cdhitInp50=tempname;
-                    [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp90 '" -o "' cdhitInp50 '" -c 0.9 -n 5 -M 2000 -aL 0.8']);
-                    if status~=0
-                        EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-                        dispEM(EM);
-                    end
-                    %Remove the old tempfile
-                    if exist(cdhitInp90, 'file')
-                        delete([cdhitInp90 '*']);
-                    end
-                    tmpFile=tempname;
-                    [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInp50 '" -o "' tmpFile '" -c 0.5 -n 3 -M 2000 -aL 0.8']);
-                    if status~=0
-                        EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
-                        dispEM(EM);
-                    end
-                    %Remove the old tempfile
-                    if exist(cdhitInp50, 'file')
-                        delete([cdhitInp50 '*']);
-                    end
-                elseif seqIdentity~=-1
+                 if seqIdentity~=-1
                     cdhitInpCustom=tempname;
                     fastawrite(cdhitInpCustom,fastaStruct);
-                    tmpFile=tempname;
                     if seqIdentity<=1 && seqIdentity>0.7
-                        [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 5 -M 2000']);
+                        nparam='5';
                     elseif seqIdentity>0.6
-                        [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 4 -M 2000']);
-                    elseif seqidentity>0.5
-                        [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 3 -M 2000']);
-                    elseif seqidentity>0.4
-                        [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n 2 -M 2000']);
+                        nparam='4';
+                    elseif seqIdentity>0.5
+                        nparam='3';
+                    elseif seqIdentity>0.4
+                        nparam='2';
                     else
                         EM='The provided seqIdentity must be between 0 and 1\n';
                         dispEM(EM);
                     end
+                    if ispc
+                        wslPath.cdhitInpCustom=getWSLpath(cdhitInpCustom);
+                        [status, output]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.cdhitInpCustom '" -o "' wslPath.tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']);
+                    elseif ismac || isunix
+                        [status, output]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' cdhitInpCustom '" -o "' tmpFile '" -c "' num2str(seqIdentity) '" -n ' nparam ' -M 2000']);
+                    end
                     if status~=0
                         EM=['Error when performing clustering of ' missingAligned{i} ':\n' output];
                         dispEM(EM);
@@ -745,7 +677,6 @@
                 else
                     %This means that CD-HIT should be skipped since
                     %seqIdentity is equal to -1
-                    tmpFile=tempname;
                     fastawrite(tmpFile,fastaStruct);
                 end
                 %Do the alignment for this file
@@ -754,7 +685,10 @@
                 elseif isunix
                     [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
                 elseif ispc
-                    [status, output]=system(['"' fullfile(ravenPath,'software','mafft','mafft-win','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' tmpFile '" > "' fullfile(dataDir,'aligned',[missingAligned{i} '.faw']) '"']);
+                    wslPath.fawFile=getWSLpath(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']));
+                    [status, ~]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --progress "' wslPath.mafftOutput '" --thread "' num2str(cores) '" --out "' wslPath.fawFile '" "' wslPath.tmpFile '"']);
+                    output=fileread(mafftOutput);
+                    delete(mafftOutput);
                 end
                 if status~=0
                     %It could be that alignment failed because only one
@@ -778,24 +712,24 @@
                 %empty file was written previously so that doesn't have to
                 %be dealt with
                 if numel(fastaStruct)==1
+                    warnState = warning; %Save the current warning state
+                    warning('off','Bioinfo:fastawrite:AppendToFile');
                     fastawrite(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fastaStruct);
+                    warning(warnState) %Reset warning state to previous settings
                 end
             end
             %Move the temporary file to the real one
             movefile(fullfile(dataDir,'aligned',[missingAligned{i} '.faw']),fullfile(dataDir,'aligned',[missingAligned{i} '.fa']),'f');
             
-            %Print the progress: no need to update this for every
-            %iteration, just report once 25%, 50% and 75% are done
-            if progressFlag==0 && i>numel(missingAligned)*0.25
-                fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.fa')))/numel(fastaFiles))*100);
-                progressFlag=progressFlag+1;
-            elseif (progressFlag==1 && i>=numel(missingAligned)*0.5) || (progressFlag==2 && i>=numel(missingAligned)*0.75)
-                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.fa')))/numel(fastaFiles))*100);
-                progressFlag=progressFlag+1;
+            %Print the progress every 25 files
+            if rem(i-1,25) == 0
+                progress=num2str(floor(100*numel(listFiles(fullfile(dataDir,'aligned','*.fa')))/numel(KOModel.rxns)));
+                progress=pad(progress,3,'left');
+                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
             end
         end
     end
-    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
 else
     if seqIdentity==-1
         fprintf('Performing the multiple alignment for KEGG Orthology specific protein sets... COMPLETE\n');
@@ -807,12 +741,8 @@
 %Check if training of Hidden Markov models should be performed
 missingHMMs=setdiff(KOModel.rxns,[hmmFiles;outFiles]);
 if ~isempty(missingHMMs)
-    fprintf('Training the KEGG Orthology specific HMMs... ');
+    fprintf('Training the KEGG Orthology specific HMMs...   0%% complete');
     missingHMMs=missingHMMs(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingHMMs)));
-    progressFlag=0;
-    %Update alignedFiles. This is needed once rebuilding KEGG from FTP dump
-    %files for more accurate progress reporting
-    alignedFiles=listFiles(fullfile(dataDir,'aligned','*.fa'));
     %Train models for all missing KOs
     for i=1:numel(missingHMMs)
         %This is checked here because it could be that it is created by a
@@ -851,19 +781,16 @@
             
             %Delete the temporary file
             delete(fullfile(dataDir,'hmms',[missingHMMs{i} '.hmw']));
-            
-            %Print the progress: no need to update this for every
-            %iteration, just report once 25%, 50% and 75% are done
-            if progressFlag==0 && i>numel(missingHMMs)*0.25
-                fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.hmm')))/numel(alignedFiles))*100);
-                progressFlag=progressFlag+1;
-            elseif (progressFlag==1 && i>=numel(missingHMMs)*0.5) || (progressFlag==2 && i>=numel(missingHMMs)*0.75)
-                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(dataDir,'*.hmm')))/numel(alignedFiles))*100);
-                progressFlag=progressFlag+1;
+
+            %Print the progress every 25 files
+            if rem(i-1,25) == 0
+                progress=num2str(floor(100*numel(listFiles(fullfile(dataDir,'hmms','*.hmm')))/numel(KOModel.rxns)));
+                progress=pad(progress,3,'left');
+                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
             end
         end
     end
-    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
 else
     fprintf('Training the KEGG Orthology specific HMMs... COMPLETE\n');
 end
@@ -872,12 +799,8 @@
 %Hidden Markov models should be performed
 missingOUT=setdiff(KOModel.rxns,outFiles);
 if ~isempty(missingOUT)
-    fprintf(['Querying ' strrep(fastaFile,'\','/') ' against the KEGG Orthology specific HMMs... ']);
+    fprintf('Querying the user-specified FASTA file against the KEGG Orthology specific HMMs...   0%% complete');
     missingOUT=missingOUT(randperm(RandStream.create('mrg32k3a','Seed',cputime()),numel(missingOUT)));
-    progressFlag=0;
-    %Update hmmFiles. This is needed once rebuilding KEGG from FTP dump
-    %files for more accurate progress reporting
-    hmmFiles=listFiles(fullfile(dataDir,'hmms','*.hmm'));
     for i=1:numel(missingOUT)
         %This is checked here because it could be that it is created by a
         %parallel process
@@ -914,20 +837,17 @@
             fwrite(fid,output);
             fclose(fid);
             
-            %Print the progress: no need to update this for every
-            %iteration, just report once 25%, 50% and 75% are done
-            if progressFlag==0 && i>numel(missingOUT)*0.25
-                fprintf('%*.*f%% complete',5,2,(numel(listFiles(fullfile(outDir,'*.out')))/numel(hmmFiles))*100);
-                progressFlag=progressFlag+1;
-            elseif (progressFlag==1 && i>=numel(missingOUT)*0.5) || (progressFlag==2 && i>=numel(missingOUT)*0.75)
-                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\b%*.*f%% complete',5,2,(numel(listFiles(fullfile(outDir,'*.out')))/numel(hmmFiles))*100);
-                progressFlag=progressFlag+1;
+            %Print the progress every 25 files
+            if rem(i-1,25) == 0
+                progress=num2str(floor(100*numel(listFiles(fullfile(outDir,'*.out')))/numel(KOModel.rxns)));
+                progress=pad(progress,3,'left');
+                fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
             end
         end
     end
-    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
+    fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');
 else
-    fprintf(['Querying ' fastaFile ' against the KEGG Orthology specific HMMs... COMPLETE\n']);
+    fprintf('Querying the user-specified FASTA file against the KEGG Orthology specific HMMs... COMPLETE\n');
 end
 
 
@@ -1108,6 +1028,8 @@
         model.rxnNotes(i)={'Included by getKEGGModelForOrganism (using HMMs)'};
     end
 end
+%Remove the temp fasta file
+delete(fastaFile)
 fprintf('COMPLETE\n\n*** Model reconstruction complete ***\n');
 end
 
diff --git a/external/kegg/getWSLpath.m b/external/kegg/getWSLpath.m
new file mode 100644
index 00000000..b989caa4
--- /dev/null
+++ b/external/kegg/getWSLpath.m
@@ -0,0 +1,19 @@
+function path=getWSLpath(path)
+% getWSLpath
+%   Translate Windows-style path to its Unix WSL (Windows Subsystem for
+%   Linux) equivalent.
+%
+%   Input:
+%   path        string with directory of file path, in Windows-style (e.g.
+%               'C:\Directory\')
+%
+%   Output:
+%   path        string with directory of file path, in Unix style (e.g.
+%               '/mnt/c/Directory/')
+%
+%   Uses the WSL function 'wslpath' to translate the path.
+%
+%   Usage: path=getWSLpath(path)
+[~,path]=system(['wsl wslpath ''' path '''']);
+path=path(1:end-1);% Remove final character (line-break)
+end
diff --git a/external/kegg/keggGenes.mat b/external/kegg/keggGenes.mat
index 33a349d3..809cdc14 100644
Binary files a/external/kegg/keggGenes.mat and b/external/kegg/keggGenes.mat differ
diff --git a/external/kegg/keggMets.mat b/external/kegg/keggMets.mat
index e415d3b0..1f86d788 100644
Binary files a/external/kegg/keggMets.mat and b/external/kegg/keggMets.mat differ
diff --git a/external/kegg/keggPhylDist.mat b/external/kegg/keggPhylDist.mat
index f190cf85..f170ef86 100644
Binary files a/external/kegg/keggPhylDist.mat and b/external/kegg/keggPhylDist.mat differ
diff --git a/external/kegg/keggRxns.mat b/external/kegg/keggRxns.mat
index 5a587f67..4e19b048 100644
Binary files a/external/kegg/keggRxns.mat and b/external/kegg/keggRxns.mat differ
diff --git a/external/metacyc/getMetaCycModelForOrganism.m b/external/metacyc/getMetaCycModelForOrganism.m
index fcc3b600..87be4cf0 100755
--- a/external/metacyc/getMetaCycModelForOrganism.m
+++ b/external/metacyc/getMetaCycModelForOrganism.m
@@ -58,7 +58,7 @@
 else
     fprintf('\nChecking existence of query FASTA file... ');
     %Check if query fasta exists
-    fastaFile=checkFileExistence(fastaFile,true,false);
+    fastaFile=checkFileExistence(fastaFile,2); %Copy file to temp dir
     fprintf('done\n');
 end
 
@@ -247,4 +247,6 @@
 [grRules,rxnGeneMat] = standardizeGrRules(model,false); %Get detailed output
 model.grRules = grRules;
 model.rxnGeneMat = rxnGeneMat;
+%Remove the temp fasta file
+delete(fastaFile)
 end
diff --git a/external/updateDocumentation.m b/external/updateDocumentation.m
index 885e9c59..beef0bf5 100755
--- a/external/updateDocumentation.m
+++ b/external/updateDocumentation.m
@@ -19,6 +19,11 @@ function updateDocumentation()
 %Get rid of MATLAB functions from external software
 ravenDirs(:,contains(ravenDirs(1,:),'software'))=[];
 
+%Remove keggModel.mat if it exists
+if exist(fullfile(ravenDir,'external','kegg','keggModel.mat'), 'file') == 2
+    delete(fullfile(ravenDir,'external','kegg','keggModel.mat'));
+end
+
 %Remove existing "doc" directory from RAVEN
 rmdir(fullfile(ravenDir,'doc'),'s');
 
diff --git a/installation/checkInstallation.m b/installation/checkInstallation.m
index 6c58bd74..6619546d 100755
--- a/installation/checkInstallation.m
+++ b/installation/checkInstallation.m
@@ -1,11 +1,20 @@
-function checkInstallation()
+function checkInstallation(develMode)
 % checkInstallation
 %   The purpose of this function is to check if all necessary functions are
 %   installed and working. It also checks whether there are any functions
 %   with overlapping names between RAVEN and other toolboxes or
 %   user-defined functions, which are accessible from MATLAB pathlist
 %
-%   Usage: checkInstallation()
+%   Input: 
+%   develMode       logical indicating development mode, which includes
+%                   testing of binaries that are required to update KEGG
+%                   HMMs (opt, default false)
+%
+%   Usage: checkInstallation(develMode)
+
+if nargin<1
+    develMode=false;
+end
 
 %Check if RAVEN is in the MATLAB path list
 paths=textscan(path,'%s','delimiter', pathsep);
@@ -22,6 +31,8 @@ function checkInstallation()
     fprintf('\n*** THE RAVEN TOOLBOX - DEVELOPMENT VERSION ***\n\n');
 end
 
+fprintf(['MATLAB R' version('-release') ' detected\n\n']);
+
 fprintf('Checking if RAVEN is on the MATLAB path...\t\t\t\t\t\t\t\t\t');
 if ismember(ravenDir,paths)
     fprintf('OK\n');
@@ -118,74 +129,29 @@ function checkInstallation()
     setRavenSolver(curSolv);
     fprintf(['WARNING: No working solver was found!\n'...
         'Install the solver, set it using setRavenSolver(''solverName'') and run checkInstallation again\n'...
-        'Available solverName options are ''mosek'', ''gurobi'' and ''cobra''\n\n']);
+        'Available solverName options are ''gurobi'' and ''cobra''\n\n']);
 end
 
-if ismac
-    binEnd='.mac';
-elseif isunix
-    binEnd='';
-elseif ispc
-    binEnd='.exe';
-end
 fprintf('Checking essential binary executables:\n');
-fprintf('NOTE: Broken binary executables must be fixed before running RAVEN\n');
-fprintf(['\tmakeblastdb' binEnd '...\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','blast+',['makeblastdb' binEnd]) '"']);
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-end
-fprintf(['\tblastp' binEnd '...\t\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','blast+',['blastp' binEnd]) '"']);
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-end
-fprintf(['\tdiamond' binEnd '...\t\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','diamond',['diamond' binEnd]) '"']);
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-end
-fprintf(['\thmmsearch' binEnd '...\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','hmmer',['hmmsearch' binEnd]) '"']);
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! Download/compile the binary and run checkInstallation again\n');
-end
-fprintf('Checking non-essential/development binary executables:\n');
-fprintf('NOTE: Only fix these binaries if planning to use KEGG FTP dump files in getKEGGModelForOrganism\n');
-fprintf(['\tcd-hit' binEnd '...\t\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','cd-hit',['cd-hit' binEnd]) '"']);
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
-end
-fprintf('\tmafft.bat...\t\t\t\t\t\t\t\t');
-if ismac
-    [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-mac','mafft.bat') '" --help ']);
-elseif isunix
-    [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-linux64','mafft.bat') '" --help ']);
-elseif ispc
-    [res,~]=system(['"' fullfile(ravenDir,'software','mafft','mafft-win','mafft.bat') '" --help ']);
-end
-if res==1
-    fprintf('OK\n');
-else
-    fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
-end
-fprintf(['\thmmbuild' binEnd '...\t\t\t\t\t\t\t\t']);
-[res,~]=system(['"' fullfile(ravenDir,'software','hmmer',['hmmbuild' binEnd]) '"']);
-if res==1
-    fprintf('OK\n\n');
-else
-    fprintf('Not OK! If necessary, download/compile the binary and run checkInstallation again\n');
+
+fprintf('\tBLAST+... ');
+res=runtests('blastPlusTests.m','OutputDetail',0);
+interpretResults(res);
+fprintf('\tDIAMOND... ');
+res=runtests('diamondTests.m','OutputDetail',0);
+interpretResults(res);
+fprintf('\tHMMER... ');
+res=runtests('hmmerTests.m','OutputDetail',0);
+interpretResults(res);
+
+if develMode
+    fprintf('NOTE: Only fix these binaries if planning to use KEGG FTP dump files in getKEGGModelForOrganism\n');
+    fprintf('\tCD-HIT... ');
+    res=runtests('cdhitTests.m','OutputDetail',0);
+    interpretResults(res);
+    fprintf('\tMAFFT... ');
+    res=runtests('mafftTests.m','OutputDetail',0);
+    interpretResults(res);
 end
 
 fprintf('Checking whether RAVEN functions are non-redundant across MATLAB path...\t');
@@ -193,3 +159,11 @@ function checkInstallation()
 
 fprintf('\n*** checkInstallation complete ***\n\n');
 end
+
+function interpretResults(results)
+if results.Failed==0 && results.Incomplete==0
+    fprintf('OK\n');
+else
+    fprintf('Not OK! Download/compile the binary and rerun checkInstallation\n');
+end
+end
diff --git a/io/checkFileExistence.m b/io/checkFileExistence.m
index 351af939..35152388 100755
--- a/io/checkFileExistence.m
+++ b/io/checkFileExistence.m
@@ -1,4 +1,4 @@
-function files=checkFileExistence(files,makeFullPath,allowSpace)
+function files=checkFileExistence(files,fullOrTemp,allowSpace)
 % checkFileExistence
 %   Check whether files exist. If no full path is given a file should be
 %   located in the current folder, which by default is appended to the
@@ -7,16 +7,23 @@
 %   Input:
 %   files           string or cell array of strings with path to file(s) or
 %                   path or filename(s)
-%   makeFullPath    logical, whether files located in the current folder
-%                   should be provided with the full path (opt, default
-%                   true)
+%   fullOrTemp      0: do not change path to file(s)
+%                   1: return full path to file(s)
+%                   2: copy file(s) to system default temporary folder and
+%                      return full path
+%                   (opt, default 0)
 %   allowSpace      logical, whether 'space' character is allowed in the
 %                   path (opt, default true)
+%
+%   Output:
+%   files           string or cell array of strings with updated paths if
+%                   fullOrTemp was set as 1 or 2, otherwise original paths
+%                   are returned
 %   
-%   Usage: files=checkFileExistence(files,makeFullPath,allowSpace)
+%   Usage: files=checkFileExistence(files,fullOrTemp,allowSpace)
 
 if nargin<2
-    makeFullPath = true;
+    fullOrTemp = 0;
 end
 if nargin<3
     allowSpace = true;
@@ -30,20 +37,36 @@
 end
 filesOriginal = files;
 
-inCurrDir = ~contains(files,'\') & ~contains(files,'/');
+%Make all full paths before check of file existence
+if ispc % full path starts like "C:\"
+    inCurrDir = cellfun(@isempty,regexpi(files,'^[a-z]\:\\'));
+else %isunix full path starts like "/"
+    inCurrDir = cellfun(@isempty,regexpi(files,'\/'));
+end
 files(inCurrDir) = fullfile(cd,files(inCurrDir));
 
+%Check existence
 for i=1:numel(files)
     if ~exist(files{i},'file')
         error('File "%s" cannot be found\n',files{i});
-    elseif allowSpace == true & strfind(files{i},' ')
+    elseif allowSpace == false & strfind(files{i},' ')
         error('File "%s" has an invalid space in the filename or path, please remove this before running this function\n',files{i});
     end
 end
 
-if makeFullPath == false
-    files = filesOriginal;
+switch fullOrTemp
+    case 0
+        files = filesOriginal;
+    case 1
+        % files already contains full path
+    case 2
+        for i=1:numel(files)
+            tmpFile=tempname;
+            copyfile(files{i},tmpFile);
+            files{i}=tmpFile;
+        end
 end
+
 if oneFile == true
     files = files{1};
 end
\ No newline at end of file
diff --git a/io/exportForGit.m b/io/exportForGit.m
index e7da5112..c273929d 100755
--- a/io/exportForGit.m
+++ b/io/exportForGit.m
@@ -1,4 +1,4 @@
-function out=exportForGit(model,prefix,path,formats,masterFlag,subDirs)
+function out=exportForGit(model,prefix,path,formats,mainBranchFlag,subDirs)
 % exportForGit
 %   Generates a directory structure and populates this with model files, ready
 %   to be commited to a Git(Hub) maintained model repository. Writes the model
@@ -13,8 +13,8 @@
 %   formats             cell array of strings specifying in what file formats
 %                       the model should be exported (opt, default to all
 %                       formats as {'mat', 'txt', 'xlsx', 'xml', 'yml'})
-%   masterFlag          logical, if true, function will error if RAVEN (and
-%                       COBRA if detected) is/are not on the master branch.
+%   mainBranchFlag          logical, if true, function will error if RAVEN (and
+%                       COBRA if detected) is/are not on the main branch.
 %                       (opt, default false)
 %   subDirs             logical, whether model files for each file format 
 %                       should be written in its own subdirectory, with
@@ -22,12 +22,12 @@
 %                       standard-GEM repository format. If false, all files
 %                       are stored in the same folder. (opt, default true)
 %
-%   Usage: exportForGit(model,prefix,path,formats,masterFlag)
+%   Usage: exportForGit(model,prefix,path,formats,mainBranchFlag)
 if nargin<6
     subDirs=true;
 end
 if nargin<5
-    masterFlag=false;
+    mainBranchFlag=false;
 end
 if nargin<4 || isempty(formats)
     formats={'mat', 'txt', 'xlsx', 'xml', 'yml'};
@@ -46,9 +46,12 @@
     prefix='model';
 end
 
+%Sort reactions, metabolites and genes alphabetically
+model=sortIdentifiers(model);
+
 %Get versions or commits of toolboxes:
-RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',masterFlag);
-COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',masterFlag);
+RAVENver = getToolboxVersion('RAVEN','ravenCobraWrapper.m',mainBranchFlag);
+COBRAver = getToolboxVersion('COBRA','initCobraToolbox.m',mainBranchFlag);
 
 %Retrieve libSBML version:
 try % 5.17.0 and newer
diff --git a/io/exportModel.m b/io/exportModel.m
index fa9c64ed..be5b64ea 100755
--- a/io/exportModel.m
+++ b/io/exportModel.m
@@ -1,4 +1,4 @@
-function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
+function exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
 % exportModel
 %   Exports a constraint-based model to an SBML file (L3V1 FBCv2)
 %
@@ -10,15 +10,23 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
 %                       (opt, default false)
 %   supressWarnings     true if warnings should be supressed (opt, default
 %                       false)
+%   sortIds             logical whether metabolites, reactions and genes
+%                       should be sorted alphabetically by their
+%                       identifiers (opt, default false)
 %
-%
-%   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings)
+%   Usage: exportModel(model,fileName,exportGeneComplexes,supressWarnings,sortIds)
 if nargin<3
     exportGeneComplexes=false;
 end
 if nargin<4
     supressWarnings=false;
 end
+if nargin<5
+    sortIds=false;
+end
+if sortIds==true
+    model=sortIdentifiers(model);
+end
 
 %If no subSystems are defined, then no need to use groups package
 if isfield(model,'subSystems')
@@ -222,7 +230,7 @@ function exportModel(model,fileName,exportGeneComplexes,supressWarnings)
     end
     
     if isfield(modelSBML.compartment,'metaid')
-        if ~isnan(str2double(model.comps(i)))
+        if regexp(model.comps{i},'^[^a-zA-Z_]')
             EM='The compartment IDs are in numeric format. For the compliance with SBML specifications, compartment IDs will be preceded with "c_" string';
             dispEM(EM,false);
             model.comps(i)=strcat('c_',model.comps(i));
diff --git a/io/exportToExcelFormat.m b/io/exportToExcelFormat.m
index d15a006b..75a6cd34 100755
--- a/io/exportToExcelFormat.m
+++ b/io/exportToExcelFormat.m
@@ -1,4 +1,4 @@
-function exportToExcelFormat(model,filename)
+function exportToExcelFormat(model,filename,sortIds)
 % exportToExcelFormat
 %   Exports a model structure to the Microsoft Excel model format
 %
@@ -8,6 +8,9 @@ function exportToExcelFormat(model,filename)
 %               be only a path, in which case the model is exported to a set
 %               of tab-delimited text files instead. See exportToTabDelimited
 %               for details regarding that functionality
+%   sortIds     logical whether metabolites, reactions and genes should be
+%               sorted alphabetically by their identifiers (opt, default
+%               false)
 %
 %   The resulting Excel file can be used with importExcelModel/SBMLFromExcel
 %   for modelling or to generate a SBML file.
@@ -15,7 +18,13 @@ function exportToExcelFormat(model,filename)
 %   NOTE: No checks are made regarding the correctness of the model. Use
 %         checkModelStruct to identify problems in the model structure
 %
-%   Usage: exportToExcelFormat(model,filename)
+%   Usage: exportToExcelFormat(model,filename,sortIds)
+if nargin<3
+    sortIds=false;
+end
+if sortIds==true
+    model=sortIdentifiers(model);
+end
 
 [~, A, B]=fileparts(filename);
 
diff --git a/io/exportToTabDelimited.m b/io/exportToTabDelimited.m
index b015bad1..137f7601 100755
--- a/io/exportToTabDelimited.m
+++ b/io/exportToTabDelimited.m
@@ -1,4 +1,4 @@
-function exportToTabDelimited(model,path)
+function exportToTabDelimited(model,path,sortIds)
 % exportToTabDelimited
 %   Exports a model structure to a set of tab-delimited text files
 %
@@ -6,6 +6,8 @@ function exportToTabDelimited(model,path)
 %   path	the path to export to. The resulting text files will be saved
 %           under the names excelRxns.txt, excelMets.txt, excelGenes.txt,
 %           excelModel.txt, and excelComps.txt
+%   sortIds logical whether metabolites, reactions and genes should be
+%           sorted alphabetically by their identifiers (opt, default false)
 %
 %   NOTE: This functionality was previously a part of exportToExcelFormat.
 %         The naming of the resulting text files is to preserve backward
@@ -14,11 +16,17 @@ function exportToTabDelimited(model,path)
 %   NOTE: No checks are made regarding the correctness of the model. Use
 %         checkModelStruct to identify problems in the model structure
 %
-%   Usage: exportToTabDelimited(model,path)
+%   Usage: exportToTabDelimited(model,path,sortIds)
 
 if nargin<2
     path='./';
 end
+if nargin<3
+    sortIds=false;
+end
+if sortIds==true
+    model=sortIdentifiers(model);
+end
 
 %If the folder doesn't exist then create it
 if ~exist(path,'dir')
diff --git a/io/getMD5Hash.m b/io/getMD5Hash.m
new file mode 100755
index 00000000..2499b089
--- /dev/null
+++ b/io/getMD5Hash.m
@@ -0,0 +1,55 @@
+function md5Hash=getMD5Hash(inputFile,binEnd)
+% getMD5Hash
+%   Calculates MD5 hash for a file
+%
+%   Input:
+%   inputFile       string with the path to file for which MD5 hash should
+%                   be calculated
+%   binEnd          string that shows the operating system running in the
+%                   client's computer. Use ".exe" for Windows, ".mac" for
+%                   macOS or leave it blank for Linux (""). (opt, by
+%                   default the function automatically detects the client's
+%                   operating system)
+%
+%   Output:
+%   md5Hash         string containing an MD5 hash for inputFile
+%   
+%   Usage: md5Hash=getMD5Hash(inputFile,binEnd)
+
+if nargin<2
+    if isunix
+        if ismac
+            binEnd='.mac';
+        else
+            binEnd='';
+        end
+    elseif ispc
+        binEnd='.exe';
+    else
+        dispEM('Unknown OS, exiting.')
+        return
+    end
+end
+
+%Check if binEnd is valid
+if ~strcmp(binEnd,'.mac') && ~strcmp(binEnd,'') && ~strcmp(binEnd,'.exe')
+   dispEM('Unknown OS, exiting.')
+   return
+end
+
+%Check file existence
+inputFile=checkFileExistence(inputFile);
+
+%Get string containing an MD5 hash
+switch binEnd
+    case '.mac'
+        [~, md5HashMessage]=system(['md5 "' inputFile '"']);
+    case ''
+        [~, md5HashMessage]=system(['md5sum "' inputFile '"']);
+    case '.exe'
+        [~, md5HashMessage]=system(['certutil -hashfile "' inputFile '" MD5"']);
+end
+
+%Extract MD5 hash from a string
+md5Hash = char(regexp(md5HashMessage,'[a-f0-9]{32}','match'));
+end
diff --git a/io/getToolboxVersion.m b/io/getToolboxVersion.m
index 729e31b6..4c9b4b69 100755
--- a/io/getToolboxVersion.m
+++ b/io/getToolboxVersion.m
@@ -1,4 +1,4 @@
-function version = getToolboxVersion(toolbox,fileID,masterFlag)
+function version = getToolboxVersion(toolbox,fileID,mainBranchFlag)
 % getToolboxVersion
 %   Returns the version of a given toolbox, or if not available the latest
 %   commit hash (7 characters).
@@ -6,16 +6,16 @@
 %   toolbox         string with the toolbox name (e.g. "RAVEN")
 %   fileID          string with the name of a file that is only found in
 %                   the corresponding toolbox (e.g. "ravenCobraWrapper.m").
-%   masterFlag      logical, if true, function will error if the toolbox is
-%                   not on the master branch (opt, default false).
+%   mainBranchFlag      logical, if true, function will error if the toolbox is
+%                   not on the main branch (opt, default false).
 %
 %   version         string containing either the toolbox version or latest
 %                   commit hash (7 characters).
 %
-%   Usage: version = getToolboxVersion(toolbox,fileID,masterFlag)
+%   Usage: version = getToolboxVersion(toolbox,fileID,mainBranchFlag)
 
 if nargin<3
-    masterFlag = false;
+    mainBranchFlag = false;
 end
 
 currentPath = pwd;
@@ -38,12 +38,12 @@
     disp([toolbox ' toolbox cannot be found'])
     version = 'unknown';
 end
-%Check if in master:
-if masterFlag
+%Check if in main:
+if mainBranchFlag
     currentBranch = git('rev-parse --abbrev-ref HEAD');
-    if ~strcmp(currentBranch,'master')
+    if any([strcmp(currentBranch, "main"), strcmp(currentBranch, "master")])
         cd(currentPath);
-        error(['ERROR: ' toolbox ' not in master. Check-out the master branch of ' toolbox ' before submitting model for Git.'])
+        error(['ERROR: ' toolbox ' not in main (or master) branch. Check-out this branch of ' toolbox ' before submitting model for Git.'])
     end
 end
 %Try to find version file of the toolbox:
diff --git a/io/sortIdentifiers.m b/io/sortIdentifiers.m
new file mode 100644
index 00000000..2974a9eb
--- /dev/null
+++ b/io/sortIdentifiers.m
@@ -0,0 +1,25 @@
+function newModel = sortIdentifiers(model)
+% exportModel
+%   Sort reactions, metabolites, genes and compartments alphabetically by
+%   their identifier.
+%
+%   Input:
+%   model       a model structure
+%
+%   Output:
+%   newModel    an updated model structure with alphabetically sorted
+%               identifiers
+%
+%   Usage: newModel=sortIdentifiers(model)
+
+[~,I]=sort(model.rxns);
+newModel=permuteModel(model,I,'rxns');
+[~,I]=sort(newModel.mets);
+newModel=permuteModel(newModel,I,'mets');
+if isfield(newModel,'genes')
+    [~,I]=sort(newModel.genes);
+    newModel=permuteModel(newModel,I,'genes');
+end
+[~,I]=sort(newModel.comps);
+newModel=permuteModel(newModel,I,'comps');
+end
\ No newline at end of file
diff --git a/io/writeYaml.m b/io/writeYaml.m
index 1a29ccdd..0f5199d6 100755
--- a/io/writeYaml.m
+++ b/io/writeYaml.m
@@ -19,7 +19,6 @@ function writeYaml(model,name,preserveQuotes,sortIds)
 if nargin < 4
     sortIds = false;
 end
-
 if ~endsWith(name,{'.yml','.yaml'})
     name = strcat(name,'.yml');
 end
@@ -29,6 +28,11 @@ function writeYaml(model,name,preserveQuotes,sortIds)
     model = ravenCobraWrapper(model);
 end
 
+%Sort identifiers alphabetically
+if sortIds == true
+    model = sortIdentifiers(model);
+end
+
 %Simplify Miriam fields:
 if isfield(model,'metMiriams')
     [model.newMetMiriams,model.newMetMiriamNames]   = extractMiriam(model.metMiriams);
@@ -56,11 +60,6 @@ function writeYaml(model,name,preserveQuotes,sortIds)
 
 %Metabolites:
 fprintf(fid,'- metabolites:\n');
-if sortIds==true
-    [~,pos] = sort(model.mets);
-else
-    pos = 1:numel(model.mets);
-end
 for i = 1:length(model.mets)
     fprintf(fid,'    - !!omap\n');
     writeField(model, fid, 'mets',        'txt', pos(i), '  - id',          preserveQuotes)
@@ -75,11 +74,6 @@ function writeYaml(model,name,preserveQuotes,sortIds)
 
 %Reactions:
 fprintf(fid,'- reactions:\n');
-if sortIds==true
-    [~,pos] = sort(model.rxns);
-else
-    pos = 1:numel(model.rxns);
-end
 for i = 1:length(model.rxns)
     fprintf(fid,'    - !!omap\n');
     writeField(model, fid, 'rxns',                 'txt', pos(i), '  - id',                    preserveQuotes)
@@ -101,11 +95,6 @@ function writeYaml(model,name,preserveQuotes,sortIds)
 
 %Genes:
 fprintf(fid,'- genes:\n');
-if sortIds==true
-    [~,pos] = sort(model.genes);
-else
-    pos = 1:numel(model.genes);
-end
 for i = 1:length(model.genes)
     fprintf(fid,'    - !!omap\n');
     writeField(model, fid, 'genes',          'txt', pos(i), '  - id',         preserveQuotes)
@@ -115,11 +104,6 @@ function writeYaml(model,name,preserveQuotes,sortIds)
 
 %Compartments:
 fprintf(fid,'- compartments: !!omap\n');
-if sortIds==true
-    [~,pos] = sort(model.comps);
-else
-    pos = 1:numel(model.comps);
-end
 for i = 1:length(model.comps)
     writeField(model, fid, 'compNames',   'txt', pos(i), ['- ' model.comps{pos(i)}], preserveQuotes)
     writeField(model, fid, 'compMiriams', 'txt', pos(i), '- annotation',             preserveQuotes)
diff --git a/software/blast+/blastp b/software/blast+/blastp
index 56cc7479..807f90c2 100755
Binary files a/software/blast+/blastp and b/software/blast+/blastp differ
diff --git a/software/blast+/blastp.exe b/software/blast+/blastp.exe
old mode 100755
new mode 100644
index e7fa489a..3927fb36
Binary files a/software/blast+/blastp.exe and b/software/blast+/blastp.exe differ
diff --git a/software/blast+/blastp.mac b/software/blast+/blastp.mac
index b82607f6..c94f53aa 100755
Binary files a/software/blast+/blastp.mac and b/software/blast+/blastp.mac differ
diff --git a/software/blast+/makeblastdb b/software/blast+/makeblastdb
index 5817d20c..d191a43d 100755
Binary files a/software/blast+/makeblastdb and b/software/blast+/makeblastdb differ
diff --git a/software/blast+/makeblastdb.exe b/software/blast+/makeblastdb.exe
old mode 100755
new mode 100644
index d0ee5c16..331a2bfb
Binary files a/software/blast+/makeblastdb.exe and b/software/blast+/makeblastdb.exe differ
diff --git a/software/blast+/makeblastdb.mac b/software/blast+/makeblastdb.mac
index f76fedcb..578acabf 100755
Binary files a/software/blast+/makeblastdb.mac and b/software/blast+/makeblastdb.mac differ
diff --git a/software/cd-hit/cd-hit b/software/cd-hit/cd-hit
index d4a6408d..618ad929 100755
Binary files a/software/cd-hit/cd-hit and b/software/cd-hit/cd-hit differ
diff --git a/software/cd-hit/cd-hit.exe b/software/cd-hit/cd-hit.exe
deleted file mode 100755
index 715d4888..00000000
Binary files a/software/cd-hit/cd-hit.exe and /dev/null differ
diff --git a/software/cd-hit/cd-hit.mac b/software/cd-hit/cd-hit.mac
index 3147efe5..6e7f77e9 100755
Binary files a/software/cd-hit/cd-hit.mac and b/software/cd-hit/cd-hit.mac differ
diff --git a/software/cd-hit/cyggcc_s-seh-1.dll b/software/cd-hit/cyggcc_s-seh-1.dll
deleted file mode 100755
index 1ab74c94..00000000
Binary files a/software/cd-hit/cyggcc_s-seh-1.dll and /dev/null differ
diff --git a/software/cd-hit/cyggomp-1.dll b/software/cd-hit/cyggomp-1.dll
deleted file mode 100755
index f2914549..00000000
Binary files a/software/cd-hit/cyggomp-1.dll and /dev/null differ
diff --git a/software/cd-hit/cygstdc++-6.dll b/software/cd-hit/cygstdc++-6.dll
deleted file mode 100755
index 75235e90..00000000
Binary files a/software/cd-hit/cygstdc++-6.dll and /dev/null differ
diff --git a/software/cd-hit/cygwin1.dll b/software/cd-hit/cygwin1.dll
deleted file mode 100755
index 3a196edb..00000000
Binary files a/software/cd-hit/cygwin1.dll and /dev/null differ
diff --git a/software/cd-hit/cygz.dll b/software/cd-hit/cygz.dll
deleted file mode 100755
index 07392898..00000000
Binary files a/software/cd-hit/cygz.dll and /dev/null differ
diff --git a/software/diamond/LICENSE b/software/diamond/LICENSE
index f288702d..ed990f8c 100644
--- a/software/diamond/LICENSE
+++ b/software/diamond/LICENSE
@@ -618,57 +618,4 @@ an absolute waiver of all civil liability in connection with the
 Program, unless a warranty or assumption of liability accompanies a
 copy of the Program in return for a fee.
 
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
-
-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-state the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    
-    Copyright (C)   
-
-    This program is free software: you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation, either version 3 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
-
-    You should have received a copy of the GNU General Public License
-    along with this program.  If not, see .
-
-Also add information on how to contact you by electronic and paper mail.
-
-  If the program does terminal interaction, make it output a short
-notice like this when it starts in an interactive mode:
-
-      Copyright (C)   
-    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, your program's commands
-might be different; for a GUI interface, you would use an "about box".
-
-  You should also get your employer (if you work as a programmer) or school,
-if any, to sign a "copyright disclaimer" for the program, if necessary.
-For more information on this, and how to apply and follow the GNU GPL, see
-.
-
-  The GNU General Public License does not permit incorporating your program
-into proprietary programs.  If your program is a subroutine library, you
-may consider it more useful to permit linking proprietary applications with
-the library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.  But first, please read
-.
+                     END OF TERMS AND CONDITIONS
\ No newline at end of file
diff --git a/software/diamond/diamond b/software/diamond/diamond
index 36736af9..546b8e06 100755
Binary files a/software/diamond/diamond and b/software/diamond/diamond differ
diff --git a/software/diamond/diamond.exe b/software/diamond/diamond.exe
old mode 100755
new mode 100644
index 0051e585..ad36d58b
Binary files a/software/diamond/diamond.exe and b/software/diamond/diamond.exe differ
diff --git a/software/diamond/diamond.mac b/software/diamond/diamond.mac
index ac4a0742..b5e1c833 100755
Binary files a/software/diamond/diamond.mac and b/software/diamond/diamond.mac differ
diff --git a/software/hmmer/LICENSE b/software/hmmer/LICENSE
index 4a2b1745..663d4f55 100644
--- a/software/hmmer/LICENSE
+++ b/software/hmmer/LICENSE
@@ -1,7 +1,7 @@
 HMMER - Biological sequence analysis with profile hidden Markov models
-Copyright (C) 1992-2019 Sean R. Eddy
-Copyright (C) 2000-2019 Howard Hughes Medical Institute
-Copyright (C) 2015-2019 President and Fellows of Harvard College
+Copyright (C) 1992-2020 Sean R. Eddy
+Copyright (C) 2000-2020 Howard Hughes Medical Institute
+Copyright (C) 2015-2020 President and Fellows of Harvard College
 Copyright (C) 1992-2004 Washington University School of Medicine
 Copyright (C) 1992-1994 MRC Laboratory of Molecular Biology
 -----------------------------------------------------------------------
@@ -90,3 +90,4 @@ BSD three-clause license:
 
 
    
+
diff --git a/software/hmmer/cygwin1.dll b/software/hmmer/cygwin1.dll
index dce2caef..350a74ba 100644
Binary files a/software/hmmer/cygwin1.dll and b/software/hmmer/cygwin1.dll differ
diff --git a/software/hmmer/hmmbuild b/software/hmmer/hmmbuild
index cc51cda0..a6f81a95 100755
Binary files a/software/hmmer/hmmbuild and b/software/hmmer/hmmbuild differ
diff --git a/software/hmmer/hmmbuild.exe b/software/hmmer/hmmbuild.exe
index 00c9d6bf..950a8394 100644
Binary files a/software/hmmer/hmmbuild.exe and b/software/hmmer/hmmbuild.exe differ
diff --git a/software/hmmer/hmmbuild.mac b/software/hmmer/hmmbuild.mac
index 25c71efe..1f457757 100755
Binary files a/software/hmmer/hmmbuild.mac and b/software/hmmer/hmmbuild.mac differ
diff --git a/software/hmmer/hmmsearch b/software/hmmer/hmmsearch
index 85330817..ab090fdc 100755
Binary files a/software/hmmer/hmmsearch and b/software/hmmer/hmmsearch differ
diff --git a/software/hmmer/hmmsearch.exe b/software/hmmer/hmmsearch.exe
index 15998cf2..66856d57 100644
Binary files a/software/hmmer/hmmsearch.exe and b/software/hmmer/hmmsearch.exe differ
diff --git a/software/hmmer/hmmsearch.mac b/software/hmmer/hmmsearch.mac
index 4fbe585d..0f393cfd 100755
Binary files a/software/hmmer/hmmsearch.mac and b/software/hmmer/hmmsearch.mac differ
diff --git a/software/mafft/mafft-linux64/mafftdir/bin/mafft b/software/mafft/mafft-linux64/mafftdir/bin/mafft
index 2c86f603..cc0af8e6 100755
--- a/software/mafft/mafft-linux64/mafftdir/bin/mafft
+++ b/software/mafft/mafft-linux64/mafftdir/bin/mafft
@@ -1,7 +1,7 @@
 #! /bin/bash 
 er=0;
 myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.467 (2020/May/14)"; export version
+version="v7.490 (2021/Oct/30)"; export version
 LANG=C; export LANG
 os=`uname`
 progname=`basename "$0"`
@@ -257,6 +257,7 @@ laraparams="/dev/null"
 foldalignopt=" "
 treealg=" -X 0.1 "
 sueff="1.0"
+maxambiguous="1.0"
 scoreoutarg=" "
 numthreads=0
 numthreadsit=-1
@@ -293,6 +294,7 @@ enrich=0        # ato de kezuru
 enrichseq=0     # ato de kezuru
 enrichstr=0     # ato de kezuru
 seektarget=""   # ato de kezuru
+dashserver="https://sysimm.org/dash/REST1.0/"
 newdash=0
 newdash_originalsequenceonly=0
 exclude_ho=0
@@ -405,6 +407,9 @@ if [ $# -gt 0 ]; then
 			shift   
 			sueff="$1"
 			treealg=" -X $1"
+		elif [ "$1" = "--maxambiguous" ]; then
+			shift   
+			maxambiguous="$1"
 		elif [ "$1" = "--noscore" ]; then
 			scorecalcopt=" -Z "
 		elif [ "$1" = "--6mermultipair" ]; then
@@ -946,8 +951,15 @@ if [ $# -gt 0 ]; then
 #			seektarget="-str"
 		elif [ "$1" = "--dash" ]; then
 			newdash=1
-			distance="global" # can be override
-			iterate=3         # can be override
+			if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct
+				distance="global"
+			fi
+			if [ "$iterate" -eq 0 ]; then # 2021/Oct
+				iterate=3
+			fi
+		elif [ "$1" = "--dashserver" ]; then
+			shift
+			dashserver="$1"
 		elif [ "$1" = "--originalseqonly" ]; then
 			newdash_originalsequenceonly=1
 		elif [ "$1" = "--excludehomologs" ]; then # works with --dash only
@@ -1030,7 +1042,7 @@ if [ $# -gt 0 ]; then
 		TMPFILE=`cygpath -w "$TMPFILE"`  # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
 	fi
 
-	umask 077
+#	umask 077  # 2021/Jan
 #	mkdir  "$TMPFILE"  || er=1
 
 
@@ -1046,7 +1058,7 @@ function removetmpfile() { # for MPI
 	if [ $debug -eq 1 ]; then
 #		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
 #		trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15
-		trap "tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
+		trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
 	else
 #		trap "rm -rf $TMPFILE" 0 15
 		trap "removetmpfile" 0 15
@@ -1065,8 +1077,16 @@ function removetmpfile() { # for MPI
 
 			cat "$1"              | tr "\r" "\n" > "$TMPFILE/infile"
 			echo ""                             >> "$TMPFILE/infile"
-			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" >> "$TMPFILE/infile"
 			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile"
+
+			if [ $maxambiguous != "1.0" ]; then
+				mv "$TMPFILE/infile" "$TMPFILE/_tofilter"
+				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1
+				mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter"
+				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1
+			fi
+			cat "$TMPFILE/_addfile" >> "$TMPFILE/infile"
+
 			cat "$scorematrix"    | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx"
 			cat "$mergetable"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable"
 			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree"
@@ -1077,11 +1097,19 @@ function removetmpfile() { # for MPI
 			cat "$anchorfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
 
 			SAVEIFS=$IFS
-			IFS='\n'
-			filelist="$1\n$addfile\n$scorematrix\n$mergetable\n$treeinfile\n$seedtablefile\n$laraparams\n$pdblist\n$ownlist"
+# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19
+			IFS=$'\n'
+			filelist="$1
+$addfile
+$scorematrix
+$mergetable
+$treeinfile
+$seedtablefile
+$laraparams
+$pdblist
+$ownlist"
 			for f in $filelist; do
-				# $f="" demo mudani file ga hashiru.
-				file "$f" 2>/dev/null | grep "UTF-[13][62]" >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
+				file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
 			done
 			IFS=$SAVEIFS
 
@@ -1095,7 +1123,7 @@ function removetmpfile() { # for MPI
 				shift
 				if [ -r "$1" ]; then
 					cat "$1" | tr "\r" "\n" >  "$TMPFILE/seed$#"
-					file "$1" | grep "UTF-[13][62]" >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
+					file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
 				else
 					echo "$0": Cannot open "$1". 1>&2
 					echo "" 1>&2
@@ -1182,7 +1210,9 @@ function removetmpfile() { # for MPI
 		exit 1;
 	fi
 
+
 	if [ "$addarg0" != " " ]; then
+
 #		iterate=0  # 2013/03/23 -> commented out, 2017/12
 		"$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile"
 		nadd=`awk '{print $1}' "$TMPFILE/addsize"`
@@ -1297,6 +1327,13 @@ function removetmpfile() { # for MPI
 			echo "npair = " $npair             1>>"$progressfile"
 			echo "nseq = " $nseq               1>>"$progressfile"
 			echo "nlen = " $nlen               1>>"$progressfile"
+
+			if [ $norg -eq 0 ]; then
+				echo "" 1>>"$progressfile"
+				echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile"
+				echo "" 1>>"$progressfile"
+				exit 1;
+			fi
 # nagasa check!
 #
 			if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then  # 2017/Oct 
@@ -1319,6 +1356,11 @@ function removetmpfile() { # for MPI
 		exit 1;
 	fi
 
+	if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+
 	if [ $allowshift -eq 1 ]; then
 		if [ $unalignspecified -ne 1 ]; then
 			unalignlevel="0.8"
@@ -1937,6 +1979,7 @@ function removetmpfile() { # for MPI
 	fi
 
 
+
 	if [ $nadd -gt "0" ]; then
 		if [ $fragment -eq "1" ]; then
 			addarg="$addarg0 $nadd -g -0.01"
@@ -1964,12 +2007,13 @@ function removetmpfile() { # for MPI
 			bunkatsuopt=" -B "  # fftnsi demo bunktasu shinai
 			if [ "$add2ndhalfarg" != " " ]; then
 				if [ $auto -eq 1 -o $iterate -gt 0 ]; then
-					echo '' 1>>"$progressfile"
-					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
-					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
-					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
-					echo '' 1>>"$progressfile"
-					exit 1
+#					echo '' 1>>"$progressfile"
+#					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
+#					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
+#					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
+#					echo '' 1>>"$progressfile"
+#					exit 1
+					iterate=0
 				fi
 			fi
 		fi
@@ -2171,6 +2215,7 @@ function removetmpfile() { # for MPI
 #		echo "iterate = " $iterate        1>>"$progressfile"
 #		echo "cycle = " $cycle            1>>"$progressfile"
 
+
 		if [ $anysymbol -eq 1 ]; then
 			mv infile orig
 			"$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
@@ -2317,7 +2362,8 @@ function removetmpfile() { # for MPI
 			if [ $anysymbol -eq 1 ]; then
 				mv orig infile # replaceu wo mukouka
 			fi
-			sed 's/-//g' infile > dashin # gap nozoku
+#			sed 's/-//g' infile > dashin # gap nozoku
+			awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin
 
 			if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
 				echo ""       1>&2
@@ -2332,11 +2378,11 @@ function removetmpfile() { # for MPI
 			fi
 			
 			echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
-			"$prefix/dash_client" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
+			"$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
 			dashres="$?"
 			if [ $dashres -ne "0" ]; then
 				echo "Error in DASH" 1>>"$progressfile"
-				echo "To use this feature, compiled with" 1>>"$progressfile"
+				echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile"
 				exit 1;
 			fi
 
@@ -2908,8 +2954,8 @@ BEGIN {
 		while( 1 )
 		{
 			go = 0;
-			printf( "OK?\n" ) > "/dev/tty";
-			printf( "@ [Y] " ) > "/dev/tty";
+			printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
 			res = getline < "/dev/tty";
 			close( "/dev/tty" );
 			if( res == 0 )
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/addsingle b/software/mafft/mafft-linux64/mafftdir/libexec/addsingle
index a1de066d..11a61d6d 100755
Binary files a/software/mafft/mafft-linux64/mafftdir/libexec/addsingle and b/software/mafft/mafft-linux64/mafftdir/libexec/addsingle differ
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/contrafoldwrap b/software/mafft/mafft-linux64/mafftdir/libexec/contrafoldwrap
index 80e14330..0e1beac9 100755
Binary files a/software/mafft/mafft-linux64/mafftdir/libexec/contrafoldwrap and b/software/mafft/mafft-linux64/mafftdir/libexec/contrafoldwrap differ
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/countlen b/software/mafft/mafft-linux64/mafftdir/libexec/countlen
index 5bb872d9..0efbbab1 100755
Binary files a/software/mafft/mafft-linux64/mafftdir/libexec/countlen and b/software/mafft/mafft-linux64/mafftdir/libexec/countlen differ
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dash_alignments b/software/mafft/mafft-linux64/mafftdir/libexec/dash_alignments
new file mode 100644
index 00000000..6047f59e
--- /dev/null
+++ b/software/mafft/mafft-linux64/mafftdir/libexec/dash_alignments
@@ -0,0 +1,483 @@
+Query 3J5P_A||281||579 Template 3J5P_A||281||579
+QUERY           EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+QUERY                                                                                                                                                                                                                                                                                                                      
+TEMPL           EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+TEMPL                                                                                                                                                                                                                                                                                                                      
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 3J5P_A||283||585 Template 3J5P_A||283||585
+QUERY           NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+QUERY                                                                                                                                                                                                                                                                                                                          
+TEMPL           NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+TEMPL                                                                                                                                                                                                                                                                                                                          
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 3J9P_A||1089||1399 Template 3J9P_A||1089||1399
+QUERY           YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL
+QUERY                                                                                                                                                                                                                                                                                                                                  
+TEMPL           YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL
+TEMPL                                                                                                                                                                                                                                                                                                                                  
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 3J9P_A||1091||1408 Template 3J9P_A||1091||1408
+QUERY           PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD
+QUERY                                                                                                                                                                                                                                                                                                                                         
+TEMPL           PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD
+TEMPL                                                                                                                                                                                                                                                                                                                                         
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 3J9P_A||1092||1402 Template 3J9P_A||1092||1402
+QUERY           LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW
+QUERY                                                                                                                                                                                                                                                                                                                                  
+TEMPL           LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW
+TEMPL                                                                                                                                                                                                                                                                                                                                  
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 3J9P_A||1096||1410 Template 3J9P_A||1096||1410
+QUERY           NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK
+QUERY                                                                                                                                                                                                                                                                                                                                      
+TEMPL           NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK
+TEMPL                                                                                                                                                                                                                                                                                                                                      
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5AN8_A||277||586 Template 5AN8_A||277||586
+QUERY           NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+QUERY                                                                                                                                                                                                                                                                                                                                 
+TEMPL           NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+TEMPL                                                                                                                                                                                                                                                                                                                                 
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5IRX_A||286||584 Template 5IRX_A||286||584
+QUERY           EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+QUERY                                                                                                                                                                                                                                                                                                                      
+TEMPL           EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+TEMPL                                                                                                                                                                                                                                                                                                                      
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5IRX_A||288||590 Template 5IRX_A||288||590
+QUERY           NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+QUERY                                                                                                                                                                                                                                                                                                                          
+TEMPL           NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+TEMPL                                                                                                                                                                                                                                                                                                                          
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5IWK_A||287||613 Template 5IWK_A||287||613
+QUERY           DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP
+QUERY                                                                                                                                                                                                                                                                                                                                                  
+TEMPL           DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP
+TEMPL                                                                                                                                                                                                                                                                                                                                                  
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5IWK_A||383||608 Template 5IWK_A||383||608
+QUERY           LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP
+QUERY                                                                                                                                                                                                                                             
+TEMPL           LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP
+TEMPL                                                                                                                                                                                                                                             
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5K47_A||19||514 Template 5K47_A||19||514
+QUERY           GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+TEMPL           GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5K47_A||20||521 Template 5K47_A||20||521
+QUERY           TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
+TEMPL           TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5K47_A||247||526 Template 5K47_A||247||526
+QUERY           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+QUERY                                                                                                                                                                                                                                                                                                   
+TEMPL           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+TEMPL                                                                                                                                                                                                                                                                                                   
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5K47_A||2||537 Template 5K47_A||2||537
+QUERY           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+TEMPL           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5K47_A||30||525 Template 5K47_A||30||525
+QUERY           REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+TEMPL           REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5MKF_A||158||704 Template 5MKF_A||158||704
+QUERY           EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
+TEMPL           EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5MKF_A||185||720 Template 5MKF_A||185||720
+QUERY           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+TEMPL           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5MKF_A||430||709 Template 5MKF_A||430||709
+QUERY           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+QUERY                                                                                                                                                                                                                                                                                                   
+TEMPL           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+TEMPL                                                                                                                                                                                                                                                                                                   
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5TJA_A||3||217 Template 5TJA_A||3||217
+QUERY           GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE
+QUERY                                                                                                                                                                                                                                  
+TEMPL           GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE
+TEMPL                                                                                                                                                                                                                                  
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5VKQ_A||1228||1596 Template 5VKQ_A||1228||1596
+QUERY           DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV
+QUERY                                                                                                                                                                                                                                                                                                                                                                                            
+TEMPL           DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                            
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5W3S_A||14||541 Template 5W3S_A||14||541
+QUERY           HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+TEMPL           HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5W3S_A||28||546 Template 5W3S_A||28||546
+QUERY           PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
+TEMPL           PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5WJ9_A||16||557 Template 5WJ9_A||16||557
+QUERY           LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+TEMPL           LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5WPV_A||16||557 Template 5WPV_A||16||557
+QUERY           LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+TEMPL           LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||127||515 Template 5Z1W_A||127||515
+QUERY           YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                
+TEMPL           YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||13||506 Template 5Z1W_A||13||506
+QUERY           SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+TEMPL           SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||246||537 Template 5Z1W_A||246||537
+QUERY           NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE
+QUERY                                                                                                                                                                                                                                                                                                               
+TEMPL           NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE
+TEMPL                                                                                                                                                                                                                                                                                                               
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||29||447 Template 5Z1W_A||29||447
+QUERY           NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                              
+TEMPL           NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                              
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||41||508 Template 5Z1W_A||41||508
+QUERY           LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
+TEMPL           LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z1W_A||9||528 Template 5Z1W_A||9||528
+QUERY           HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+TEMPL           HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z96_A||286||659 Template 5Z96_A||286||659
+QUERY           LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                 
+TEMPL           LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                 
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z96_A||289||660 Template 5Z96_A||289||660
+QUERY           LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI
+QUERY                                                                                                                                                                                                                                                                                                                                                                                               
+TEMPL           LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                               
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5Z96_A||290||663 Template 5Z96_A||290||663
+QUERY           KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                 
+TEMPL           KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                 
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5ZX5_A||814||1056 Template 5ZX5_A||814||1056
+QUERY           FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+QUERY                                                                                                                                                                                                                                                              
+TEMPL           FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+TEMPL                                                                                                                                                                                                                                                              
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5ZX5_A||820||1131 Template 5ZX5_A||820||1131
+QUERY           LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+QUERY                                                                                                                                                                                                                                                                                                                                   
+TEMPL           LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+TEMPL                                                                                                                                                                                                                                                                                                                                   
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5ZX5_A||821||1134 Template 5ZX5_A||821||1134
+QUERY           DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+QUERY                                                                                                                                                                                                                                                                                                                                     
+TEMPL           DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+TEMPL                                                                                                                                                                                                                                                                                                                                     
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 5ZX5_A||827||1228 Template 5ZX5_A||827||1228
+QUERY           NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                             
+TEMPL           NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                             
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6A70_A||27||559 Template 6A70_A||27||559
+QUERY           SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
+TEMPL           SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6A70_A||284||563 Template 6A70_A||284||563
+QUERY           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+QUERY                                                                                                                                                                                                                                                                                                   
+TEMPL           NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+TEMPL                                                                                                                                                                                                                                                                                                   
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6A70_A||39||574 Template 6A70_A||39||574
+QUERY           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+TEMPL           PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6A70_A||67||562 Template 6A70_A||67||562
+QUERY           REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+TEMPL           REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6A70_B||227||1129 Template 6A70_B||227||1129
+QUERY           LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
+TEMPL           LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6AEI_A||287||663 Template 6AEI_A||287||663
+QUERY           LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                    
+TEMPL           LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                    
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6AEI_A||290||664 Template 6AEI_A||290||664
+QUERY           LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                  
+TEMPL           LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                  
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6AEI_A||291||667 Template 6AEI_A||291||667
+QUERY           KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                    
+TEMPL           KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                    
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6AYF_A||19||546 Template 6AYF_A||19||546
+QUERY           HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+TEMPL           HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BBJ_A||424||746 Template 6BBJ_A||424||746
+QUERY           GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+QUERY                                                                                                                                                                                                                                                                                                                                              
+TEMPL           GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+TEMPL                                                                                                                                                                                                                                                                                                                                              
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BBJ_A||428||750 Template 6BBJ_A||428||750
+QUERY           SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+QUERY                                                                                                                                                                                                                                                                                                                                              
+TEMPL           SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+TEMPL                                                                                                                                                                                                                                                                                                                                              
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BCO_A||735||1081 Template 6BCO_A||735||1081
+QUERY           PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV
+QUERY                                                                                                                                                                                                                                                                                                                                                                      
+TEMPL           PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV
+TEMPL                                                                                                                                                                                                                                                                                                                                                                      
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BO5_A||314||642 Template 6BO5_A||314||642
+QUERY           NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK
+QUERY                                                                                                                                                                                                                                                                                                                                                    
+TEMPL           NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK
+TEMPL                                                                                                                                                                                                                                                                                                                                                    
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BO8_A||288||614 Template 6BO8_A||288||614
+QUERY           DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP
+QUERY                                                                                                                                                                                                                                                                                                                                                  
+TEMPL           DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP
+TEMPL                                                                                                                                                                                                                                                                                                                                                  
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BO8_A||384||609 Template 6BO8_A||384||609
+QUERY           IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP
+QUERY                                                                                                                                                                                                                                             
+TEMPL           IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP
+TEMPL                                                                                                                                                                                                                                             
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BPQ_A||570||883 Template 6BPQ_A||570||883
+QUERY           IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL
+QUERY                                                                                                                                                                                                                                                                                                                                     
+TEMPL           IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL
+TEMPL                                                                                                                                                                                                                                                                                                                                     
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BQR_A||661||1011 Template 6BQR_A||661||1011
+QUERY           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+QUERY                                                                                                                                                                                                                                                                                                                                                                          
+TEMPL           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                          
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BQV_A||739||1089 Template 6BQV_A||739||1089
+QUERY           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+QUERY                                                                                                                                                                                                                                                                                                                                                                          
+TEMPL           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                          
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWD_A||470||712 Template 6BWD_A||470||712
+QUERY           FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+QUERY                                                                                                                                                                                                                                                              
+TEMPL           FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+TEMPL                                                                                                                                                                                                                                                              
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWD_A||476||787 Template 6BWD_A||476||787
+QUERY           LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+QUERY                                                                                                                                                                                                                                                                                                                                   
+TEMPL           LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+TEMPL                                                                                                                                                                                                                                                                                                                                   
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWD_A||477||790 Template 6BWD_A||477||790
+QUERY           DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+QUERY                                                                                                                                                                                                                                                                                                                                     
+TEMPL           DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+TEMPL                                                                                                                                                                                                                                                                                                                                     
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWD_A||480||793 Template 6BWD_A||480||793
+QUERY           DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI
+QUERY                                                                                                                                                                                                                                                                                                                                     
+TEMPL           DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI
+TEMPL                                                                                                                                                                                                                                                                                                                                     
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWD_A||483||904 Template 6BWD_A||483||904
+QUERY           NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL
+QUERY                                                                                                                                                                                                                                                                                                                                                                                                                                                 
+TEMPL           NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                                                                                                 
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWI_A||536||886 Template 6BWI_A||536||886
+QUERY           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+QUERY                                                                                                                                                                                                                                                                                                                                                                          
+TEMPL           PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+TEMPL                                                                                                                                                                                                                                                                                                                                                                          
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6BWJ_A||351||680 Template 6BWJ_A||351||680
+QUERY           NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+QUERY                                                                                                                                                                                                                                                                                                                                                     
+TEMPL           NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+TEMPL                                                                                                                                                                                                                                                                                                                                                     
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6C8G_A||293||615 Template 6C8G_A||293||615
+QUERY           GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+QUERY                                                                                                                                                                                                                                                                                                                                              
+TEMPL           GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+TEMPL                                                                                                                                                                                                                                                                                                                                              
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6C8G_A||294||617 Template 6C8G_A||294||617
+QUERY           EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM
+QUERY                                                                                                                                                                                                                                                                                                                                               
+TEMPL           EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM
+TEMPL                                                                                                                                                                                                                                                                                                                                               
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6C8G_A||295||619 Template 6C8G_A||295||619
+QUERY           EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+QUERY                                                                                                                                                                                                                                                                                                                                                
+TEMPL           EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+TEMPL                                                                                                                                                                                                                                                                                                                                                
+Equivalence     9999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6C8G_A||419||661 Template 6C8G_A||419||661
+QUERY           FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN
+QUERY                                                                                                                                                                                                                                                              
+TEMPL           FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN
+TEMPL                                                                                                                                                                                                                                                              
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6CO7_A||808||1043 Template 6CO7_A||808||1043
+QUERY           EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI
+QUERY                                                                                                                                                                                                                                                       
+TEMPL           EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI
+TEMPL                                                                                                                                                                                                                                                       
+Equivalence     99999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
+Query 6CO7_A||810||1124 Template 6CO7_A||810||1124
+QUERY           REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL
+QUERY                                                                                                                                                                                                                                                                                                                                      
+TEMPL           REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL
+TEMPL                                                                                                                                                                                                                                                                                                                                      
+Equivalence     999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999999
+
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dash_client b/software/mafft/mafft-linux64/mafftdir/libexec/dash_client
index dd4ff391..e30f683e 100755
Binary files a/software/mafft/mafft-linux64/mafftdir/libexec/dash_client and b/software/mafft/mafft-linux64/mafftdir/libexec/dash_client differ
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dash_sequences.fa b/software/mafft/mafft-linux64/mafftdir/libexec/dash_sequences.fa
new file mode 100644
index 00000000..bec30a1e
--- /dev/null
+++ b/software/mafft/mafft-linux64/mafftdir/libexec/dash_sequences.fa
@@ -0,0 +1,138 @@
+>DASH_3J5P_A||281||579
+EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+>DASH_3J5P_A||283||585
+NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+>DASH_3J9P_A||1089||1399
+YEPLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKL
+>DASH_3J9P_A||1091||1408
+PLTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVD
+>DASH_3J9P_A||1092||1402
+LTALNAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLW
+>DASH_3J9P_A||1096||1410
+NAMVQNNRIELLNHPVCKEYLLMKWLAYGFRAHMMNLGSYCLGLIPMTILVVNIKPGMAFNSTGIINETSDHSEILDTTNSYLIKTCMILVFLSSIFGYCKEAGQIFQQKRNYFMDISNVLEWIIYTTGIIFVLPLFVEIPAHLQWQCGAIAVYFYWMNFLLYLQRFENCGIFIVMLEVILKTLLRSTVVFIFLLLAFGLSFYILLNLQDPFSSPLLSIIQTFSMMLGDINYRESFLEPYLRNELAHPVLSFAQLVSFTIFVPIVLMNLLIGLAVGDIADVQKHASLKRIAMQVELHTSLEKKLPLWFLRKVDQK
+>DASH_5AN8_A||277||586
+NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+>DASH_5IRX_A||286||584
+EKNSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSF
+>DASH_5IRX_A||288||590
+NSVLEVIAYSSSETPNRHDMLLVEPLNRLLQDKWDRFVKRIFYFNFFVYCLYMIIFTAAAYYRPVEGLPPYKLKNTVGDYFRVTGEILSVSGGVYFFFRGIQYFLQRRPSLKSLFVDSYSEILFFVQSLFMLVSVVLYFSQRKEYVASMVFSLAMGWTNMLYYTRGFQQMGIYAVMIEKMILRDLCRFMFVYLVFLFGFSTAVVTLIEDGKYNSLYSTCLELFKFTIGMGDLEFTENYDFKAVFIILLLAYVILTYILLLNMLIALMGETVNKIAQESKNIWKLQRAITILDTEKSFLKCMRK
+>DASH_5IWK_A||287||613
+DDQSLLELIVTTKKREARQILDQTPVKELVSLKWKRYGRPYFCVLGAIYVLYIICFTMCCVYRPLKPRITNRTNPRDNTLLQQKLLQEAYVTPKDDLRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLPRCLWP
+>DASH_5IWK_A||383||608
+LRLVGELVSIVGAVIILLVEIPDIFRLGVTRFFGQTILGGPFHVIIVTYAFMVLVTMVMRLTNSDGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWQMAVVILGFASAFYIIFQTEDPDELGHFYDYPMALFSTFELFLTIIDGPANYDVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQVVATTVMLERKLP
+>DASH_5K47_A||19||514
+GTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAE
+>DASH_5K47_A||20||521
+TRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+>DASH_5K47_A||247||526
+NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+>DASH_5K47_A||2||537
+PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+>DASH_5K47_A||30||525
+REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+>DASH_5MKF_A||158||704
+EDQGPPCPSPVGGGDPLHRHLPLEGQPPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLI
+>DASH_5MKF_A||185||720
+PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+>DASH_5MKF_A||430||709
+NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+>DASH_5TJA_A||3||217
+GLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSLE
+>DASH_5VKQ_A||1228||1596
+DKRNVEFLDVLIENEQKEVIAHTVVQRYLQELWHGSLTWASWKILLLLVAFIVCPPVWIGFTFPMGHKFNKVPIIKFMSYLTSHIYLMIHLSIVGITPIYPVLRLSLVPYWYEVGLLIWLSGLLLFELTNPSDKSGLGSIKVLVLLLGMAGVGVHVSAFLFVSKEYWPTLVYCRNQCFALAFLLACVQILDFLSFHHLFGPWAIIIGDLLKDLARFLAVLAIFVFGFSMHIVALNQSFANFSPEDLRSFEKKNRNRGYFSDVRMHPINSFELLFFAVFGQTTTEQTQVDKIKNVATPTQPYWVEYLFKIVFGIYMLVSVVVLIQLLIAMMSDTYQRIQAQSDIEWKFGLSKLIRNMHRTTTAPSPLNLV
+>DASH_5W3S_A||14||541
+HEEENRCNFNQHTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLED
+>DASH_5W3S_A||28||546
+PSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTVAFKHLFLKGYIDRMDDTYAVYTQSDVYDQIIFAVNQYLQLYQVSVGNHAYENKGTDQSAMAICQHFYKRGNIYPGNDTFDIDPEIETDCFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHNMMIFDAFVILTCLVSLILCIRSVISGLQLQQEFVNFFLLHYKKDVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHNKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKHYQQDGFPETELRTFISECKDLPNSGKFRLEDDPPVS
+>DASH_5WJ9_A||16||557
+LTPNPGYGTQAGPSPAPPTPPEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLAVTFREENTIAFRHLFLLGYSDGADDTFAAYTREQLYQAIFHAVDQYLALPDVSLGRYAYVRGGGDPWTNGSGLALCQRYYHRGHVDPANDTFDIDPMVVTDCIQVDPPERPPPPPSDDLTLLESSSSYKNLTLKFHKLVNVTIHFRLKTINLQSLINNEIPDCYTFSVLITFDNKAHSGRIPISLETQAHIQECKHPSVFQHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVGFMWRQRGRVISLWERLEFVNGWYILLVTSDVLTISGTIMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHNYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGRSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGAGAEESELQAYIAQCQDSPTSGKFRRGS
+>DASH_5WPV_A||16||557
+LTPNPGYGTQVGTSPAPTTPTEEEDLRRRLKYFFMSPCDKFRAKGRKPCKLMLQVVKILVVTVQLILFGLSNQLVVTFREENTIAFRHLFLLGYSDGSDDTFAAYTQEQLYQAIFYAVDQYLILPEISLGRYAYVRGGGGPWANGSALALCQRYYHRGHVDPANDTFDIDPRVVTDCIQVDPPDRPPDIPSEDLDFLDGSASYKNLTLKFHKLINVTIHFQLKTINLQSLINNEIPDCYTFSILITFDNKAHSGRIPIRLETKTHIQECKHPSVSRHGDNSFRLLFDVVVILTCSLSFLLCARSLLRGFLLQNEFVVFMWRRRGREISLWERLEFVNGWYILLVTSDVLTISGTVMKIGIEAKNLASYDVCSILLGTSTLLVWVGVIRYLTFFHKYNILIATLRVALPSVMRFCCCVAVIYLGYCFCGWIVLGPYHVKFRSLSMVSECLFSLINGDDMFVTFAAMQAQQGHSSLVWLFSQLYLYSFISLFIYMVLSLFIALITGAYDTIKHPGGTGTEKSELQAYIEQCQDSPTSGKFRRGS
+>DASH_5Z1W_A||127||515
+YENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQL
+>DASH_5Z1W_A||13||506
+SIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKE
+>DASH_5Z1W_A||246||537
+NANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKTLLRLRLRKE
+>DASH_5Z1W_A||29||447
+NRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFV
+>DASH_5Z1W_A||41||508
+LVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEEL
+>DASH_5Z1W_A||9||528
+HICRSIRGLWGTTLTENTAENRELYVKTTLRELVVYIVFLVDICLLTYGMTSSSAYYYTKVMSELFLHTPSDSGVSFQTISSMSDFWDFAQGPLLDSLYWTKWYNNQSLGRGSHSFIYYENLLLGAPRLRQLRVRNDSCVVHEDFREDILNCYDVYSPDKEDQLPFGPQNGTAWTYHSQNELGGSSHWGRLTSYSGGGYYLDLPGSRQASAEALQGLQEGLWLDRGTRVVFIDFSVYNANINLFCILRLVVEFPATGGTIPSWQIRTVKLIRYVNNWDFFIVGCEVVFCVFIFYYVVEEILEIHLHRLRYLSSVWNILDLVVILLSIVAVGFHIFRTLEVNRLMGKLLQQPDTYADFEFLAFWQTQYNNMNAVNLFFAWIKIFKYISFNKTMTQLSSTLARCAKDILGFAIMFFIVFFAYAQLGYLLFGTQVENFSTFVKCIFTQFRIILGDFDYNAIDNANRILGPVYFVTYVFFVFFVLLNMFLAIINDTYSEVKEELAGQKDQLQLSDFLKQSYNKT
+>DASH_5Z96_A||286||659
+LARLKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNV
+>DASH_5Z96_A||289||660
+LKLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVI
+>DASH_5Z96_A||290||663
+KLAIKYRQKEFVAQPNCQQLLASRWYDEFPGWRRRHWAVKMVTCFIIGLLFPVFSVCYLIAPKSPLGLFIRKPFIKFICHTASYLTFLFLLLLASQHIDRSDLNRQGPPPTIVEWMILPWVLGFIWGEIKQMWDGGLQDYIHDWWNLMDFVMNSLYLATISLKIVAFVKYSALNPRESWDMWHPTLVAEALFAIANIFSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYEETKGLSCKGIRCEKQNNAFSTLFETLQSLFWSIFGLINLYVTNVKAQHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFEEGGTLPTPFNVIPSP
+>DASH_5ZX5_A||814||1056
+FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+>DASH_5ZX5_A||820||1131
+LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+>DASH_5ZX5_A||821||1134
+DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+>DASH_5ZX5_A||827||1228
+NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLD
+>DASH_6A70_A||27||559
+SHPQFEKGSAAAPRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIR
+>DASH_6A70_A||284||563
+NANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYH
+>DASH_6A70_A||39||574
+PRVAWAERLVRGLRGLWGTRLMEESSTNREKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGYHKALVKLKLKKN
+>DASH_6A70_A||67||562
+REKYLKSVLRELVTYLLFLIVLCILTYGMMSSNVYYYTRMMSQLFLDTPVSKTEKTNFKTLSSMEDFWKFTEGSLLDGLYWKMQPSNQTEADNRSFIFYENLLLGVPRIRQLRVRNGSCSIPQDLRDEIKECYDVYSVSSEDRAPFGPRNGTAWIYTSEKDLNGSSHWGIIATYSGAGYYLDLSRTREETAAQVASLKKNVWLDRGTRATFIDFSVYNANINLFCVVRLLVEFPATGGVIPSWQFQPLKLIRYVTTFDFFLAACEIIFCFFIFYYVVEEILEIRIHKLHYFRSFWNCLDVVIVVLSVVAIGINIYRTSNVEVLLQFLEDQNTFPNFEHLAYWQIQFNNIAAVTVFFVWIKLFKFINFNRTMSQLSTTMSRCAKDLFGFAIMFFIIFLAYAQLAYLVFGTQVDDFSTFQECIFTQFRIILGDINFAEIEEANRVLGPIYFTTFVFFMFFILLNMFLAIINDTYSEVKSDLAQQKAEMELSDLIRKGY
+>DASH_6A70_B||227||1129
+LRFRRLLVAELQRGFFDKHIWLSIWDRPPRSRFTRIQRATCCVLLICLFLGANAVWYGAVGDSAYSTGHVSRLSPLSVDTVAVGLVSSVVVYPVYLAILFLFRMSRSKVAGSPSPTPAGQQVLDIDSCLDSSVLDSSFLTFSGLHAEQAFVGQMKSDLFLDDSKSLVCWPSGEGTLSWPDLLSDPSIVGSNLRQLARGQAGHGLGPEEDGFSLASPYSPAKSFSASDEDLIQQVLAEGVSSPAPTQDTHMETDLLSSLSSTPGEKTETLALQRLGELGPPSPGLNWEQPQAARLSRTGLVEGLRKRLLPAWCASLAHGLSLLLVAVAVAVSGWVGASFPPGVSVAWLLSSSASFLASFLGWEPLKVLLEALYFSLVAKRLHPDEDDTLVESPAVTPVSARVPRVRPPHGFALFLAKEEARKVKRLHGMLRSLLVYMLFLLVTLLASYGDASCHGHAYRLQSAIKQELHSRAFLAITRSEELWPWMAHVLLPYVHGNQSSPELGPPRLRQVRLQEALYPDPPGPRVHTCSAAGGFSTSDYDVGWESPHNGSGTWAYSAPDLLGAWSWGSCAVYDSGGYVQELGLSLEESRDRLRFLQLHNWLDNRSRAVFLELTRYSPAVGLHAAVTLRLEFPAAGRALAALSVRPFALRRLSAGLSLPLLTSVCLLLFAVHFAVAEARTWHREGRWRVLRLGAWARWLLVALTAATALVRLAQLGAADRQWTRFVRGRPRRFTSFDQVAQLSSAARGLAASLLFLLLVKAAQQLRFVRQWSVFGKTLCRALPELLGVTLGLVVLGVAYAQLAILLVSSCVDSLWSVAQALLVLCPGTGLSTLCPAESWHLSPLLCVGLWALRLWGALRLGAVILRWRYHALRGELYRPAWEPQDYEMVELFLRRLRLWMGLSK
+>DASH_6AEI_A||287||663
+LAKLKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNI
+>DASH_6AEI_A||290||664
+LKVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNII
+>DASH_6AEI_A||291||667
+KVAIKYHQKEFVAQPNCQQLLATLWYDGFPGWRRKHWVVKLLTCMTIGFLFPMLSIAYLISPRSNLGLFIKKPFIKFICHTASYLTFLFMLLLASQHIVRTDLHVQGPPPTVVEWMILPWVLGFIWGEIKEMWDGGFTEYIHDWWNLMDFAMNSLYLATISLKIVAYVKYNGSRPREEWEMWHPTLIAEALFAISNILSSLRLISLFTANSHLGPLQISLGRMLLDILKFLFIYCLVLLAFANGLNQLYFYYETRAIDEPNNCKGIRCEKQNNAFSTLFETLQSLFWSVFGLLNLYVTNVKARHEFTEFVGATMFGTYNVISLVVLLNMLIAMMNNSYQLIADHADIEWKFARTKLWMSYFDEGGTLPPPFNIIPSP
+>DASH_6AYF_A||19||546
+HEEENRCNFNQQTSPSEELLLEDQMRRKLKFFFMNPCEKFWARGRKPWKLAIQILKIAMVTIQLVLFGLSNQMVVAFKEENTIAFKHLFLKGYMDRMDDTYAVYTQSDVYDQLIFAVNQYLQLYNVSVGNHAYENKGTKQSAMAICQHFYKRGNIYPGNDTFDIDPEIETECFFVEPDEPFHIGTPAENKLNLTLDFHRLLTVELQFKLKAINLQTVRHQELPDCYDFTLTITFDNKAHSGRIKISLDNDISIRECKDWHVSGSIQKNTHYMMIFDAFVILTCLVSLILCIRSVIRGLQLQQEFVNFFLLHYKKEVSVSDQMEFVNGWYIMIIISDILTIIGSILKMEIQAKSLTSYDVCSILLGTSTMLVWLGVIRYLGFFAKYNLLILTLQAALPNVIRFCCCAAMIYLGYCFCGWIVLGPYHDKFRSLNMVSECLFSLINGDDMFATFAKMQQKSYLVWLFSRIYLYSFISLFIYMILSLFIALITDTYETIKQYQQDGFPETELRTFISECKDLPNSGKYRLED
+>DASH_6BBJ_A||424||746
+GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+>DASH_6BBJ_A||428||750
+SVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSNCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+>DASH_6BCO_A||735||1081
+PPGTVEPSAKVALERRQRRRPGRALCCGKFSKRWSDFWGAPVTAFLGNVVSYLLFLLLFAHVLLVDFQPTKPSVSELLLYFWAFTLLCEELRQGLGGGWGSLASGGRGPDRAPLRHRLHLYLSDTWNQCDLLALTCFLLGVGCRLTPGLFDLGRTVLCLDFMIFTLRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLCVWLVAYGVATEGILRPQDRSLPSILRRVFYRPYLQIFGQIPQEEMDVALMIPGNCSMERGSWAHPEGPVAGSCVSQYANWLVVLLLIVFLLVANILLLNLLIAMFSYTFSKVHGNSDLYWKAQRYSLIREFHSRPALAPPLIIISHV
+>DASH_6BO5_A||314||642
+NSVLEIIAFHCKSPNRHRMVVLEPLNKLLQEKWDRLVSRFFFNFACYLVYMFIFTVVAYHQPSLDQPAIPSSKATFGESMLLLGHILILLGGIYLLLGQLWYFWRRRLFIWISFMDSYFEILFLLQALLTVLSQVLRFMETEWYLPLLVLSLVLGWLNLLYYTRGFQHTGIYSVMIQKVILRDLLRFLLVYLVFLFGFAVALVSLSREARSPKAPEDNNSTVTEQPTVGQEEEPAPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNHVADNSWSIWKLQKAISVLEMENGYWWCRRKK
+>DASH_6BO8_A||288||614
+DEQSLLELIITTKKREARQILDQTPVKELVSLKWKRYGRPYFCMLGAIYLLYIICFTMCCIYRPLKPRTNNRTSPRDNTLLQQKLLQEAYMTPKDDIRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLPRCLWP
+>DASH_6BO8_A||384||609
+IRLVGELVTVIGAIIILLVEVPDIFRMGVTRFFGQTILGGPFHVLIITYAFMVLVTMVMRLISASGEVVPMSFALVLGWCNVMYFARGFQMLGPFTIMIQKMIFGDLMRFCWLMAVVILGFASAFYIIFQTEDPEELGHFYDYPMALFSTFELFLTIIDGPANYNVDLPFMYSITYAAFAIIATLLMLNLLIAMMGDTHWRVAHERDELWRAQIVATTVMLERKLP
+>DASH_6BPQ_A||570||883
+IILCLFFFPLIGCGFISFRKKPVEKTKKLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIILYVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLAIFYFIAGIVFRLHSDESSWYSGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAVWMVAFGVARQGILRKNEHRWEWIFRSVIYEPYLAMFGQYPDDIDGTTYNFDHCTFSGNESKPLCVELDANNQPRFPEWITIPLVCIYMLSTNILLVNLLVAMFGYTVGSVQENNDQVWKFQRFFLVQEYCSRL
+>DASH_6BQR_A||661||1011
+PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+>DASH_6BQV_A||739||1089
+PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+>DASH_6BWD_A||470||712
+FKEVKILDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCA
+>DASH_6BWD_A||476||787
+LDSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPL
+>DASH_6BWD_A||477||790
+DSSDGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIIL
+>DASH_6BWD_A||480||793
+DGKNEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHI
+>DASH_6BWD_A||483||904
+NEMEIHIKSKKLPITRKFYAFYHAPIVKFWFNTLAYLGFLMLYTFVVLVKMEQLPSVQEWIVIAYIFTYAIEKVREVFMSEAGKISQKIKVWFSDYFNVSDTIAIISFFVGFGLRFGAKWNYINAYDNHVFVAGRLIYCLNIIFWYVRLLDFLAVNQQAGPYVMMIGKMVANMFYIVVIMALVLLSFGVPRKAILYPHEEPSWSLAKDIVFHPYWMIFGEVYAYEIDVCANDSTLPTICGPGTWLTPFLQAVYLFVQYIIMVNLLIAFFNNVYLQVKAISNIVWKYQRYHFIMAYHEKPVLPPPLIILSHIVSLFCCVCKRRKKDKTSDGPKLFLTEEDQKKLHDFEEQCVEMYFDEKDDKFNSGSEERIRVTFERVEQMSIQIKEVGDRVNYIKRSLQSLDSQIGHLQDLSALTVDTLKTL
+>DASH_6BWI_A||536||886
+PVGTADPAEKTPLGVPRQSGRPGCCGGRCGGRRCLRRWFHFWGAPVTIFMGNVVSYLLFLLLFSRVLLVDFQPAPPGSLELLLYFWAFTLLCEELRQGLSGGGGSLASGGPGPGHASLSQRLRLYLADSWNQCDLVALTCFLLGVGCRLTPGLYHLGRTVLCIDFMVFTVRLLHIFTVNKQLGPKIVIVSKMMKDVFFFLFFLGVWLVAYGVATEGLLRPRDSDFPSILRRVFYRPYLQIFGQIPQEDMDVALMEHSNCSSEPGFWAHPPGAQAGTCVSQYANWLVVLLLVIFLLVANILLVNLLIAMFSYTFGKVQGNSDLYWKAQRYRLIREFHSRPALAPPFIVISHL
+>DASH_6BWJ_A||351||680
+NSVLEIIAFHSRSPHRHRMVVLEPLNKLLQAKWDRLIPRFCFNFLCYLVYMLIFTAVAYHQPALEKQGFPPLKATAGNSMLLLGHILILLGGVYLLLGQLWYFWRRRLFIWISFMDSYSEILFLLQALLTVLSQVLCFLAIEWYLPLLVSSLVMGWTNLLYYTRGFQHTGIYSVMIEKVILRDLLRFLLVYLVFLFGFAVALVSLSREAQNSRTPAGPNATEVGQPGAGQEDEAPPYRSILDASLELFKFTIGMGELAFQEQLRFRGVVLLLLLAYVLLTYVLLLNMLIALMSETVNSVATDSWSIWKLQKAISVLEMENGYWWCRRKKQ
+>DASH_6C8G_A||293||615
+GEEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPV
+>DASH_6C8G_A||294||617
+EEVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCM
+>DASH_6C8G_A||295||619
+EVSVLEILVYNSKVENRHEMLAVEPINELLRDKWQKFGAVSFYISVVSYLIAMIIFTLIAYYRPMDGTPPYPYRTTMDYMRLAGEIVTLLTGVVFFITNIKDLFMKKCPGVNSLFIDGSFQLLYFIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRK
+>DASH_6C8G_A||419||661
+FIYSVLVIITAVLYLVGIESYLAVMVFALVLGWMNALYFTRGLKLTGTYSIMLQKILFKDLFRFLLVYLLFMIGYASALVSLLNPCTSQESCIETSSQCTVPEYPSCRDSSTFSKFLLDLFKLTIGMGDLEMINSAKYPAVFIILLVTYIILTFVLLLNMLIALMGETVGQVSKESKQIWKLQWATTILDIERSFPVCMRKAFRSGEMVTVGKNLDGTPDRRWCFRVDEVNWSHWNQNLGIIN
+>DASH_6CO7_A||808||1043
+EIREDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEI
+>DASH_6CO7_A||810||1124
+REDDSMEVIMRNKKLGFCDRIMHFYSAPFSKFVGNVVGYLAFIFLYAYVVLFNFPRFDPAKTLGGIHPTEIVLYFWVFTILIEEIRQLAAKPPKYIKDKVSVYFSDTWNFVDIFSLTVFIIAIILRFFTNSRIFTASRIILSLDIIFFIVRSLQIFSVNRLLGPKLVMIQKMMQDLAQFIIILAVFTIAYGIALHAVMFPSPGIYARNNTWVTITSVVQYPYWQMYGELFLDEIQGEKPKEFGEVDPDGRWLSPLLLAIYMVFTNILLLNLLIAIFNYTFERVQEDSDKVWKFQRYDLVQEYHSRPVFAPPLVLL
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/disttbfast b/software/mafft/mafft-linux64/mafftdir/libexec/disttbfast
index 95d397f0..4d950cf7 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dndblast b/software/mafft/mafft-linux64/mafftdir/libexec/dndblast
index 2dc2c6e0..b4b112d0 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dndfast7 b/software/mafft/mafft-linux64/mafftdir/libexec/dndfast7
index 51faee70..0ee51697 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dndpre b/software/mafft/mafft-linux64/mafftdir/libexec/dndpre
index d2ff7554..4b27abed 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/dvtditr b/software/mafft/mafft-linux64/mafftdir/libexec/dvtditr
index 370e90a1..115b2ec7 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/f2cl b/software/mafft/mafft-linux64/mafftdir/libexec/f2cl
index 286dad87..d740559a 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/filter b/software/mafft/mafft-linux64/mafftdir/libexec/filter
new file mode 100755
index 00000000..f0ad2ead
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/getlag b/software/mafft/mafft-linux64/mafftdir/libexec/getlag
index 863dc5e7..7c4ea918 100755
Binary files a/software/mafft/mafft-linux64/mafftdir/libexec/getlag and b/software/mafft/mafft-linux64/mafftdir/libexec/getlag differ
diff --git a/software/mafft/mafft-win/usr/share/misc/magic b/software/mafft/mafft-linux64/mafftdir/libexec/hat3
similarity index 100%
rename from software/mafft/mafft-win/usr/share/misc/magic
rename to software/mafft/mafft-linux64/mafftdir/libexec/hat3
diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/mafft-distance b/software/mafft/mafft-linux64/mafftdir/libexec/mafft-distance
index 32b8d77a..be7f77a2 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/mafft-profile b/software/mafft/mafft-linux64/mafftdir/libexec/mafft-profile
index 00dc0d19..73936551 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/makedirectionlist b/software/mafft/mafft-linux64/mafftdir/libexec/makedirectionlist
index a03893f6..89f3ccb3 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/mccaskillwrap b/software/mafft/mafft-linux64/mafftdir/libexec/mccaskillwrap
index 69bb00a1..85bd1665 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/multi2hat3s b/software/mafft/mafft-linux64/mafftdir/libexec/multi2hat3s
index 11aab741..4b06fcf4 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/nodepair b/software/mafft/mafft-linux64/mafftdir/libexec/nodepair
index bd38ad41..581fefea 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/pairash b/software/mafft/mafft-linux64/mafftdir/libexec/pairash
index e46be817..307a0534 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/pairlocalalign b/software/mafft/mafft-linux64/mafftdir/libexec/pairlocalalign
index d303df10..475cba76 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/regtable2seq b/software/mafft/mafft-linux64/mafftdir/libexec/regtable2seq
index 5a2b5082..45e90d17 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/replaceu b/software/mafft/mafft-linux64/mafftdir/libexec/replaceu
index b3ed3503..fcd6ab7e 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/restoreu b/software/mafft/mafft-linux64/mafftdir/libexec/restoreu
index 40271f91..ff6bbb5f 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/score b/software/mafft/mafft-linux64/mafftdir/libexec/score
index c0ec883b..c815992f 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/seq2regtable b/software/mafft/mafft-linux64/mafftdir/libexec/seq2regtable
index 46df62a8..4b2b440e 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/setcore b/software/mafft/mafft-linux64/mafftdir/libexec/setcore
index 866273b2..30472e54 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/setdirection b/software/mafft/mafft-linux64/mafftdir/libexec/setdirection
index 529e48cb..95b15080 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/sextet5 b/software/mafft/mafft-linux64/mafftdir/libexec/sextet5
index 4fd249ea..0df7bbc5 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/splittbfast b/software/mafft/mafft-linux64/mafftdir/libexec/splittbfast
index 9428a0ce..c35e2881 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/tbfast b/software/mafft/mafft-linux64/mafftdir/libexec/tbfast
index a96ad5bb..1ab0e605 100755
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diff --git a/software/mafft/mafft-linux64/mafftdir/libexec/version b/software/mafft/mafft-linux64/mafftdir/libexec/version
index 53cc6716..e30b3a86 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/bin/mafft b/software/mafft/mafft-mac/mafftdir/bin/mafft
index 3bd3a2b1..91b5fc97 100755
--- a/software/mafft/mafft-mac/mafftdir/bin/mafft
+++ b/software/mafft/mafft-mac/mafftdir/bin/mafft
@@ -1,7 +1,7 @@
 #! /bin/bash 
 er=0;
 myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.467 (2020/May/14)"; export version
+version="v7.490 (2021/Oct/30)"; export version
 LANG=C; export LANG
 os=`uname`
 progname=`basename "$0"`
@@ -257,6 +257,7 @@ laraparams="/dev/null"
 foldalignopt=" "
 treealg=" -X 0.1 "
 sueff="1.0"
+maxambiguous="1.0"
 scoreoutarg=" "
 numthreads=0
 numthreadsit=-1
@@ -293,6 +294,7 @@ enrich=0        # ato de kezuru
 enrichseq=0     # ato de kezuru
 enrichstr=0     # ato de kezuru
 seektarget=""   # ato de kezuru
+dashserver="https://sysimm.org/dash/REST1.0/"
 newdash=0
 newdash_originalsequenceonly=0
 exclude_ho=0
@@ -405,6 +407,9 @@ if [ $# -gt 0 ]; then
 			shift   
 			sueff="$1"
 			treealg=" -X $1"
+		elif [ "$1" = "--maxambiguous" ]; then
+			shift   
+			maxambiguous="$1"
 		elif [ "$1" = "--noscore" ]; then
 			scorecalcopt=" -Z "
 		elif [ "$1" = "--6mermultipair" ]; then
@@ -946,8 +951,15 @@ if [ $# -gt 0 ]; then
 #			seektarget="-str"
 		elif [ "$1" = "--dash" ]; then
 			newdash=1
-			distance="global" # can be override
-			iterate=3         # can be override
+			if [ "$distance" != "local" -a "$distance" != "localgenaf" ]; then # 2021/Oct
+				distance="global"
+			fi
+			if [ "$iterate" -eq 0 ]; then # 2021/Oct
+				iterate=3
+			fi
+		elif [ "$1" = "--dashserver" ]; then
+			shift
+			dashserver="$1"
 		elif [ "$1" = "--originalseqonly" ]; then
 			newdash_originalsequenceonly=1
 		elif [ "$1" = "--excludehomologs" ]; then # works with --dash only
@@ -1030,7 +1042,7 @@ if [ $# -gt 0 ]; then
 		TMPFILE=`cygpath -w "$TMPFILE"`  # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
 	fi
 
-	umask 077
+#	umask 077  # 2021/Jan
 #	mkdir  "$TMPFILE"  || er=1
 
 
@@ -1046,7 +1058,7 @@ function removetmpfile() { # for MPI
 	if [ $debug -eq 1 ]; then
 #		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
 #		trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15
-		trap "tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
+		trap "popd > /dev/null 2>&1; tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
 	else
 #		trap "rm -rf $TMPFILE" 0 15
 		trap "removetmpfile" 0 15
@@ -1065,8 +1077,16 @@ function removetmpfile() { # for MPI
 
 			cat "$1"              | tr "\r" "\n" > "$TMPFILE/infile"
 			echo ""                             >> "$TMPFILE/infile"
-			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" >> "$TMPFILE/infile"
 			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile"
+
+			if [ $maxambiguous != "1.0" ]; then
+				mv "$TMPFILE/infile" "$TMPFILE/_tofilter"
+				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/infile" 2>>"$progressfile" || exit 1
+				mv "$TMPFILE/_addfile" "$TMPFILE/_tofilter"
+				"$prefix/filter" -m $maxambiguous $seqtype -i "$TMPFILE/_tofilter" > "$TMPFILE/_addfile" 2>>"$progressfile" || exit 1
+			fi
+			cat "$TMPFILE/_addfile" >> "$TMPFILE/infile"
+
 			cat "$scorematrix"    | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx"
 			cat "$mergetable"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable"
 			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree"
@@ -1077,11 +1097,19 @@ function removetmpfile() { # for MPI
 			cat "$anchorfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
 
 			SAVEIFS=$IFS
-			IFS='\n'
-			filelist="$1\n$addfile\n$scorematrix\n$mergetable\n$treeinfile\n$seedtablefile\n$laraparams\n$pdblist\n$ownlist"
+# Fixed a bug: 'n' was misinterpreted as delimiter, 2020/Jun/19
+			IFS=$'\n'
+			filelist="$1
+$addfile
+$scorematrix
+$mergetable
+$treeinfile
+$seedtablefile
+$laraparams
+$pdblist
+$ownlist"
 			for f in $filelist; do
-				# $f="" demo mudani file ga hashiru.
-				file "$f" 2>/dev/null | grep "UTF-[13][62]" >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
+				file "$f" 2>/dev/null | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
 			done
 			IFS=$SAVEIFS
 
@@ -1095,7 +1123,7 @@ function removetmpfile() { # for MPI
 				shift
 				if [ -r "$1" ]; then
 					cat "$1" | tr "\r" "\n" >  "$TMPFILE/seed$#"
-					file "$1" | grep "UTF-[13][62]" >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
+					file "$1" | grep -e 'UTF-16' -e 'UTF-32' >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
 				else
 					echo "$0": Cannot open "$1". 1>&2
 					echo "" 1>&2
@@ -1182,7 +1210,9 @@ function removetmpfile() { # for MPI
 		exit 1;
 	fi
 
+
 	if [ "$addarg0" != " " ]; then
+
 #		iterate=0  # 2013/03/23 -> commented out, 2017/12
 		"$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile"
 		nadd=`awk '{print $1}' "$TMPFILE/addsize"`
@@ -1297,6 +1327,13 @@ function removetmpfile() { # for MPI
 			echo "npair = " $npair             1>>"$progressfile"
 			echo "nseq = " $nseq               1>>"$progressfile"
 			echo "nlen = " $nlen               1>>"$progressfile"
+
+			if [ $norg -eq 0 ]; then
+				echo "" 1>>"$progressfile"
+				echo "The reference sequence was removed because of ambiguous letters?" 1>>"$progressfile"
+				echo "" 1>>"$progressfile"
+				exit 1;
+			fi
 # nagasa check!
 #
 			if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then  # 2017/Oct 
@@ -1319,6 +1356,11 @@ function removetmpfile() { # for MPI
 		exit 1;
 	fi
 
+	if [ `awk "BEGIN {print( 0.0+\"$maxambiguous\" < 0.0 || 0.0+\"$maxambiguous\" > 1.0 )}"` -gt 0 ]; then
+		printf "\n%s\n\n" "The argument of --maxambiguous must be between 0.0 and 1.0" 1>>"$progressfile"
+		exit 1;
+	fi
+
 	if [ $allowshift -eq 1 ]; then
 		if [ $unalignspecified -ne 1 ]; then
 			unalignlevel="0.8"
@@ -1937,6 +1979,7 @@ function removetmpfile() { # for MPI
 	fi
 
 
+
 	if [ $nadd -gt "0" ]; then
 		if [ $fragment -eq "1" ]; then
 			addarg="$addarg0 $nadd -g -0.01"
@@ -1964,12 +2007,13 @@ function removetmpfile() { # for MPI
 			bunkatsuopt=" -B "  # fftnsi demo bunktasu shinai
 			if [ "$add2ndhalfarg" != " " ]; then
 				if [ $auto -eq 1 -o $iterate -gt 0 ]; then
-					echo '' 1>>"$progressfile"
-					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
-					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
-					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
-					echo '' 1>>"$progressfile"
-					exit 1
+#					echo '' 1>>"$progressfile"
+#					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
+#					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
+#					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
+#					echo '' 1>>"$progressfile"
+#					exit 1
+					iterate=0
 				fi
 			fi
 		fi
@@ -2171,6 +2215,7 @@ function removetmpfile() { # for MPI
 #		echo "iterate = " $iterate        1>>"$progressfile"
 #		echo "cycle = " $cycle            1>>"$progressfile"
 
+
 		if [ $anysymbol -eq 1 ]; then
 			mv infile orig
 			"$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
@@ -2317,7 +2362,8 @@ function removetmpfile() { # for MPI
 			if [ $anysymbol -eq 1 ]; then
 				mv orig infile # replaceu wo mukouka
 			fi
-			sed 's/-//g' infile > dashin # gap nozoku
+#			sed 's/-//g' infile > dashin # gap nozoku
+			awk '{if(/^>/)print; else {gsub( /-/,"" ); print;}}' infile > dashin
 
 			if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
 				echo ""       1>&2
@@ -2332,11 +2378,11 @@ function removetmpfile() { # for MPI
 			fi
 			
 			echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
-			"$prefix/dash_client" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
+			"$prefix/dash_client" -url "$dashserver" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
 			dashres="$?"
 			if [ $dashres -ne "0" ]; then
 				echo "Error in DASH" 1>>"$progressfile"
-				echo "To use this feature, compiled with" 1>>"$progressfile"
+				echo "To enable this feature, compile with DASH_CLIENT=dash_client. Go compiler is necessary." 1>>"$progressfile"
 				exit 1;
 			fi
 
@@ -2908,8 +2954,8 @@ BEGIN {
 		while( 1 )
 		{
 			go = 0;
-			printf( "OK?\n" ) > "/dev/tty";
-			printf( "@ [Y] " ) > "/dev/tty";
+			printf( "Type Y or just enter to run this command.\n" ) > "/dev/tty";
+			printf( "@ " ) > "/dev/tty";
 			res = getline < "/dev/tty";
 			close( "/dev/tty" );
 			if( res == 0 )
diff --git a/software/mafft/mafft-mac/mafftdir/libexec/addsingle b/software/mafft/mafft-mac/mafftdir/libexec/addsingle
index 57b73aca..1ff0f8f6 100755
Binary files a/software/mafft/mafft-mac/mafftdir/libexec/addsingle and b/software/mafft/mafft-mac/mafftdir/libexec/addsingle differ
diff --git a/software/mafft/mafft-mac/mafftdir/libexec/contrafoldwrap b/software/mafft/mafft-mac/mafftdir/libexec/contrafoldwrap
index f0f8cf14..1402942a 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/countlen b/software/mafft/mafft-mac/mafftdir/libexec/countlen
index b0c91349..84789f2a 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/dash_client b/software/mafft/mafft-mac/mafftdir/libexec/dash_client
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/dndblast b/software/mafft/mafft-mac/mafftdir/libexec/dndblast
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/dndfast7 b/software/mafft/mafft-mac/mafftdir/libexec/dndfast7
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/dndpre b/software/mafft/mafft-mac/mafftdir/libexec/dndpre
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/dvtditr b/software/mafft/mafft-mac/mafftdir/libexec/dvtditr
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/f2cl b/software/mafft/mafft-mac/mafftdir/libexec/f2cl
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/filter b/software/mafft/mafft-mac/mafftdir/libexec/filter
new file mode 100755
index 00000000..f5c6dd2e
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/getlag b/software/mafft/mafft-mac/mafftdir/libexec/getlag
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/hex2maffttext b/software/mafft/mafft-mac/mafftdir/libexec/hex2maffttext
index 1caa9eb4..d5a9601f 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/mafft-distance b/software/mafft/mafft-mac/mafftdir/libexec/mafft-distance
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/mafft-profile b/software/mafft/mafft-mac/mafftdir/libexec/mafft-profile
index c096fc9e..ecb9e93c 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/maffttext2hex b/software/mafft/mafft-mac/mafftdir/libexec/maffttext2hex
index ca59092d..f33f5b60 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/makedirectionlist b/software/mafft/mafft-mac/mafftdir/libexec/makedirectionlist
index 2fe6d014..53db353a 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/mccaskillwrap b/software/mafft/mafft-mac/mafftdir/libexec/mccaskillwrap
index 5feaf984..ddf86a43 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/multi2hat3s b/software/mafft/mafft-mac/mafftdir/libexec/multi2hat3s
index ad9c4944..5599e514 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/nodepair b/software/mafft/mafft-mac/mafftdir/libexec/nodepair
index 68a7de9a..acf55903 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/pairash b/software/mafft/mafft-mac/mafftdir/libexec/pairash
index ccb35c20..b64df32f 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/pairlocalalign b/software/mafft/mafft-mac/mafftdir/libexec/pairlocalalign
index c9ba3921..80e7b591 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/regtable2seq b/software/mafft/mafft-mac/mafftdir/libexec/regtable2seq
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/replaceu b/software/mafft/mafft-mac/mafftdir/libexec/replaceu
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/restoreu b/software/mafft/mafft-mac/mafftdir/libexec/restoreu
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/score b/software/mafft/mafft-mac/mafftdir/libexec/score
index d1be07fb..66977105 100755
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/seq2regtable b/software/mafft/mafft-mac/mafftdir/libexec/seq2regtable
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/setcore b/software/mafft/mafft-mac/mafftdir/libexec/setcore
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/splittbfast b/software/mafft/mafft-mac/mafftdir/libexec/splittbfast
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/tbfast b/software/mafft/mafft-mac/mafftdir/libexec/tbfast
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diff --git a/software/mafft/mafft-mac/mafftdir/libexec/version b/software/mafft/mafft-mac/mafftdir/libexec/version
index cd9f5c91..de766d27 100755
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diff --git a/software/mafft/mafft-win/mafft-signed.ps1 b/software/mafft/mafft-win/mafft-signed.ps1
deleted file mode 100755
index f09c3c70..00000000
--- a/software/mafft/mafft-win/mafft-signed.ps1
+++ /dev/null
@@ -1,176 +0,0 @@
-Write-Host;
-Write-Host Preparing environment to run MAFFT on Windows.
-Write-Host This may take a while, if real-time scanning by anti-virus software is on.
-
-Set-Item Env:Path "/usr/bin;$Env:Path"
-Set-Item Env:MAFFT_BINARIES "/usr/lib/mafft"
-Set-Item Env:TMPDIR "$Env:TMP"
-Set-Item Env:MAFFT_TMPDIR "$Env:TMP"
-Set-Item Env:mafft_working_dir "$PWD"
-
-#Set-Item Env:TMPDIR "/tmp"
-#Set-Item Env:MAFFT_TMPDIR "/tmp"
-# If you do not have write permission for standard temporary folder
-# (typically C:\Users\username\AppData\Local\Temp\), then
-# uncomment (remove #) the above two lines to use an alternative 
-# temporary folder.
-
-#$ROOTDIR=$PSScriptRoot # not supported by powershell versions <= 2
-$ROOTDIR=Split-Path -Parent $MyInvocation.MyCommand.Path
-$proc = Start-Process -Wait -NoNewWindow -PassThru -FilePath "$ROOTDIR\usr\bin\bash.exe" -ArgumentList "'/usr/bin/mafft' $args"
-exit $proc.ExitCode
-
-# SIG # Begin signature block
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-# pjzY5hjHLZ6r
-# SIG # End signature block
diff --git a/software/mafft/mafft-win/mafft.bat b/software/mafft/mafft-win/mafft.bat
deleted file mode 100755
index c674ca60..00000000
--- a/software/mafft/mafft-win/mafft.bat
+++ /dev/null
@@ -1,33 +0,0 @@
-@echo off
-setlocal enabledelayedexpansion
-cls; 1>&2
-chcp 65001 1>&2
-for /f "usebackq tokens=*" %%i IN (`cd`) DO @set current_dir=%%i
-if /i "%current_dir%" == "%systemroot%" (
-  set mafft_working_dir="%~dp0"
-) else (
-  set mafft_working_dir="%current_dir%"
-)
-pushd "%mafft_working_dir%"
-
-echo; 1>&2
-echo Preparing environment to run MAFFT on Windows. 1>&2
-echo This may take a while, if real-time scanning by anti-virus software is on. 1>&2
-
-set ROOTDIR=%~d0%~p0
-set PATH=/usr/bin/:%PATH%
-set MAFFT_BINARIES=/usr/lib/mafft
-set TMPDIR=%TMP%
-set MAFFT_TMPDIR=%TMPDIR%
-
-REM set TMPDIR=%ROOTDIR%/tmp
-REM set MAFFT_TMPDIR=%TMPDIR%
-REM If you do not have write permission for Windows temporary folder
-REM (typically C:\Users\username\AppData\Local\Temp\), then
-REM uncomment (remove REM) the above two lines to use an alternative 
-REM temporary folder.
-
-"%ROOTDIR%\usr\bin\bash" "/usr/bin/mafft" %*
-
-popd
-exit /b
diff --git a/software/mafft/mafft-win/testdata.txt b/software/mafft/mafft-win/testdata.txt
deleted file mode 100755
index bbba8ae0..00000000
--- a/software/mafft/mafft-win/testdata.txt
+++ /dev/null
@@ -1,4 +0,0 @@
->1
-acdefghijklm
->2
-ghijkm
diff --git a/software/mafft/mafft-win/usr/bin/awk.exe b/software/mafft/mafft-win/usr/bin/awk.exe
deleted file mode 100755
index ba7929a7..00000000
Binary files a/software/mafft/mafft-win/usr/bin/awk.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/basename.exe b/software/mafft/mafft-win/usr/bin/basename.exe
deleted file mode 100755
index 3e63ef79..00000000
Binary files a/software/mafft/mafft-win/usr/bin/basename.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/bash.exe b/software/mafft/mafft-win/usr/bin/bash.exe
deleted file mode 100755
index 32149dab..00000000
Binary files a/software/mafft/mafft-win/usr/bin/bash.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/cat.exe b/software/mafft/mafft-win/usr/bin/cat.exe
deleted file mode 100755
index c98a8d70..00000000
Binary files a/software/mafft/mafft-win/usr/bin/cat.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/chmod.exe b/software/mafft/mafft-win/usr/bin/chmod.exe
deleted file mode 100755
index e026d85c..00000000
Binary files a/software/mafft/mafft-win/usr/bin/chmod.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/comm.exe b/software/mafft/mafft-win/usr/bin/comm.exe
deleted file mode 100755
index 759879ef..00000000
Binary files a/software/mafft/mafft-win/usr/bin/comm.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/cp.exe b/software/mafft/mafft-win/usr/bin/cp.exe
deleted file mode 100755
index 269ce23f..00000000
Binary files a/software/mafft/mafft-win/usr/bin/cp.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/cut.exe b/software/mafft/mafft-win/usr/bin/cut.exe
deleted file mode 100755
index 55496345..00000000
Binary files a/software/mafft/mafft-win/usr/bin/cut.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/date.exe b/software/mafft/mafft-win/usr/bin/date.exe
deleted file mode 100755
index be06d12e..00000000
Binary files a/software/mafft/mafft-win/usr/bin/date.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/dirname.exe b/software/mafft/mafft-win/usr/bin/dirname.exe
deleted file mode 100755
index 10c35f3b..00000000
Binary files a/software/mafft/mafft-win/usr/bin/dirname.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/echo.exe b/software/mafft/mafft-win/usr/bin/echo.exe
deleted file mode 100755
index a6263790..00000000
Binary files a/software/mafft/mafft-win/usr/bin/echo.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/env.exe b/software/mafft/mafft-win/usr/bin/env.exe
deleted file mode 100755
index 1a194a21..00000000
Binary files a/software/mafft/mafft-win/usr/bin/env.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/expr.exe b/software/mafft/mafft-win/usr/bin/expr.exe
deleted file mode 100755
index d26179ab..00000000
Binary files a/software/mafft/mafft-win/usr/bin/expr.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/false.exe b/software/mafft/mafft-win/usr/bin/false.exe
deleted file mode 100755
index 6a5a4ae0..00000000
Binary files a/software/mafft/mafft-win/usr/bin/false.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/file.exe b/software/mafft/mafft-win/usr/bin/file.exe
deleted file mode 100755
index af6dd183..00000000
Binary files a/software/mafft/mafft-win/usr/bin/file.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/fold.exe b/software/mafft/mafft-win/usr/bin/fold.exe
deleted file mode 100755
index 967a451a..00000000
Binary files a/software/mafft/mafft-win/usr/bin/fold.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/grep.exe b/software/mafft/mafft-win/usr/bin/grep.exe
deleted file mode 100755
index a31c8871..00000000
Binary files a/software/mafft/mafft-win/usr/bin/grep.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/gzip.exe b/software/mafft/mafft-win/usr/bin/gzip.exe
deleted file mode 100755
index 766dcfb3..00000000
Binary files a/software/mafft/mafft-win/usr/bin/gzip.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/head.exe b/software/mafft/mafft-win/usr/bin/head.exe
deleted file mode 100755
index efdeb1d4..00000000
Binary files a/software/mafft/mafft-win/usr/bin/head.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/id.exe b/software/mafft/mafft-win/usr/bin/id.exe
deleted file mode 100755
index 8fef3ca5..00000000
Binary files a/software/mafft/mafft-win/usr/bin/id.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/info.exe b/software/mafft/mafft-win/usr/bin/info.exe
deleted file mode 100755
index f53a2187..00000000
Binary files a/software/mafft/mafft-win/usr/bin/info.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/join.exe b/software/mafft/mafft-win/usr/bin/join.exe
deleted file mode 100755
index 854de6fa..00000000
Binary files a/software/mafft/mafft-win/usr/bin/join.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/ln.exe b/software/mafft/mafft-win/usr/bin/ln.exe
deleted file mode 100755
index 109ba1a0..00000000
Binary files a/software/mafft/mafft-win/usr/bin/ln.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/ls.exe b/software/mafft/mafft-win/usr/bin/ls.exe
deleted file mode 100755
index 2e5e4f87..00000000
Binary files a/software/mafft/mafft-win/usr/bin/ls.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/bin/mafft b/software/mafft/mafft-win/usr/bin/mafft
deleted file mode 100755
index 3bd3a2b1..00000000
--- a/software/mafft/mafft-win/usr/bin/mafft
+++ /dev/null
@@ -1,2937 +0,0 @@
-#! /bin/bash 
-er=0;
-myself=`dirname "$0"`/`basename "$0"`; export myself
-version="v7.467 (2020/May/14)"; export version
-LANG=C; export LANG
-os=`uname`
-progname=`basename "$0"`
-windows="no"
-if [ `echo $os | grep -i cygwin` ]; then
-	os="cygwin"
-	windows="yes"
-elif [ `echo $os | grep -i msys` ]; then
-	os="msys"
-	windows="yes"
-elif [ `echo $os | grep -i mingw` ]; then
-	os="mingw"
-	windows="yes"
-elif [ `echo $os | grep -i darwin` ]; then
-	os="darwin"
-elif [ `echo $os | grep -i sunos` ]; then
-	os="sunos"
-elif [ `echo $os | grep -i linux` ]; then
-	os="linux"
-else
-	os="unix"
-fi
-#export os # iranai
-if [ "$windows" = "yes" ]; then
-	echo "" 1>&2
-	echo "It may take a while before the calculation starts" 1>&2
-	echo "if being scanned by anti-virus software." 1>&2
-	echo "Also consider using a faster version for Windows 10:" 1>&2
-	echo "https://mafft.cbrc.jp/alignment/software/wsl.html" 1>&2
-fi
-
-if [ "$MAFFT_BINARIES" ]; then
-	prefix="$MAFFT_BINARIES"
-else
-	prefix=/usr/local/libexec/mafft
-fi
-export prefix # iranai
-
-if [ $# -gt 0 ]; then
-	if [ "$1" = "--man" ]; then 
-		man "$prefix/mafft.1"
-		exit 0;
-	fi
-fi
-
-if [ -x "$prefix/version" ]; then
-#		versionbin=`"$prefix/version" | awk '{print $1}'` # for cygwin
-		versionbin=`"$prefix/version"` # for cygwin 2.7
-	else
-		versionbin="0.000"
-fi
-
-if ! expr "$version" : v"$versionbin" > /dev/null ; then
-	echo "" 1>&2
-	echo "v$versionbin != $version" 1>&2
-	echo "" 1>&2
-	echo "There is a problem in the configuration of your shell." 1>&2
-	echo "Check the MAFFT_BINARIES environmental variable by" 1>&2
-	echo "$ echo \$MAFFT_BINARIES" 1>&2
-	echo "" 1>&2
-	echo "This variable must be *unset*, unless you have installed MAFFT" 1>&2
-	echo "with a special configuration.  To unset this variable, type" 1>&2
-	echo "$ unset MAFFT_BINARIES" 1>&2
-	echo "or" 1>&2
-	echo "% unsetenv MAFFT_BINARIES" 1>&2
-	echo "Then retry" 1>&2
-	echo "$ mafft input > output" 1>&2
-	echo "" 1>&2
-	echo "To keep this change permanently, edit setting files" 1>&2
-	echo "(.bash_profile, .profile, .cshrc, etc) in your home directory" 1>&2
-	echo "to delete the MAFFT_BINARIES line." 1>&2
-	echo "On MacOSX, also edit or remove the .MacOSX/environment.plist file" 1>&2
-	echo "and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7)." 1>&2
-	echo "" 1>&2
-	echo "Please send a problem report to katoh@ifrec.osaka-u.ac.jp," 1>&2
-	echo "if this problem remains." 1>&2
-	echo "" 1>&2
-	exit 1
-	er=1
-fi
-
-defaultiterate=0
-defaultcycle=2
-defaultgop="1.53"
-#defaultaof="0.123"
-defaultaof="0.000"
-defaultlaof="0.100"
-defaultlgop="-2.00"
-defaultfft=1
-defaultrough=0
-defaultdistance="ktuples"
-#defaultdistance="local"
-defaultweighti="2.7"
-defaultweightr="0.0"
-defaultweightm="1.0"
-defaultdafs=0
-defaultmccaskill=0
-defaultcontrafold=0
-defaultalgopt="  "
-defaultalgoptit="  "
-defaultsbstmodel=" -b 62 "
-defaultfmodel=" "
-defaultkappa=" "
-if [ $progname = "xinsi" -o $progname = "mafft-xinsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="scarna"
-	defaultweighti="3.2"
-	defaultweightr="8.0"
-	defaultweightm="2.0"
-	defaultmccaskill=1
-	defaultcontrafold=0
-	defaultdafs=0
-	defaultalgopt=" -A "
-	defaultalgoptit=" -AB " ## chui
-	defaultaof="0.0"
-	defaultsbstmodel=" -b 62 "
-	defaultkappa=" "
-	defaultfmodel="    "  # 2013/06/18
-elif [ $progname = "qinsi" -o $progname = "mafft-qinsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="global"
-	defaultweighti="3.2"
-	defaultweightr="8.0"
-	defaultweightm="2.0"
-	defaultmccaskill=1
-	defaultcontrafold=0
-	defaultdafs=0
-	defaultalgopt=" -A "
-	defaultalgoptit=" -AB " ## chui
-	defaultaof="0.0"
-	defaultsbstmodel=" -b 62 "
-	defaultkappa=" "
-	defaultfmodel="    "  # 2013/06/18
-elif [ $progname = "linsi" -o $progname = "mafft-linsi" ]; then
-	defaultfft=0
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="local"
-elif [ $progname = "ginsi" -o $progname = "mafft-ginsi" ]; then
-	defaultfft=1
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="global"
-elif [ $progname = "einsi" -o $progname = "mafft-einsi" ]; then
-	defaultfft=0
-	defaultcycle=1
-	defaultiterate=1000
-	defaultdistance="localgenaf"
-elif [ $progname = "fftns" -o $progname = "mafft-fftns" ]; then
-	defaultfft=1
-	defaultcycle=2
-	defaultdistance="ktuples"
-elif [ $progname = "fftnsi" -o $progname = "mafft-fftnsi" ]; then
-	defaultfft=1
-	defaultcycle=2
-	defaultiterate=2
-	defaultdistance="ktuples"
-elif [ $progname = "nwns" -o $progname = "mafft-nwns" ]; then
-	defaultfft=0
-	defaultcycle=2
-	defaultdistance="ktuples"
-elif [ $progname = "nwnsi" -o $progname = "mafft-nwnsi" ]; then
-	defaultfft=0
-	defaultcycle=2
-	defaultiterate=2
-	defaultdistance="ktuples"
-fi
-outputfile=""
-namelength=-1
-anysymbol=0
-parallelizationstrategy="BAATARI2"
-kappa=$defaultkappa
-sbstmodel=$defaultsbstmodel
-fmodel=$defaultfmodel
-nmodel=" "
-gexp=0
-gop=$defaultgop
-gopdist=$defaultgop
-aof=$defaultaof
-cycle=$defaultcycle
-iterate=$defaultiterate
-fft=$defaultfft
-rough=$defaultrough
-distance=$defaultdistance
-forcefft=0
-memopt=" "
-weightopt=" "
-GGOP="-6.00"
-LGOP="-6.00"
-LEXP="-0.000"
-GEXP="-0.000"
-lgop=$defaultlgop
-lexp="-0.100"
-laof=$defaultlaof
-pggop="-2.00"
-pgexp="-0.10"
-pgaof="0.10"
-rgop="-1.530"
-rgep="-0.000"
-seqtype="  "
-weighti=$defaultweighti
-weightr=$defaultweightr
-weightm=$defaultweightm
-rnaalifold=0
-dafs=$defaultdafs
-mccaskill=$defaultmccaskill
-contrafold=$defaultcontrafold
-progressfile="/dev/stderr"
-anchorfile="/dev/null"
-anchoropt=""
-maxanchorseparation=1000
-debug=0
-sw=0
-algopt=$defaultalgopt
-algoptit=$defaultalgoptit
-#algspecified=0
-pairspecified=0
-scorecalcopt=" "
-coreout=0
-corethr="0.5"
-corewin="100"
-coreext=" "
-outputformat="pir"
-f2clext="-N"
-outorder="input"
-seed="x"
-seedtable="x"
-auto=0
-groupsize=-1
-partsize=50
-partdist="ktuples"
-partorderopt=" -x "
-treeout=0
-nodeout=0
-distout=0
-treein=0
-topin=0
-treeinopt="  "
-seedfiles="/dev/null"
-seedtablefile="/dev/null"
-pdblist="/dev/null"
-ownlist="/dev/null"
-strdir="$PWD"
-scorematrix="/dev/null"
-textmatrix="/dev/null"
-treeinfile="/dev/null"
-rnascoremtx=" "
-laraparams="/dev/null"
-foldalignopt=" "
-treealg=" -X 0.1 "
-sueff="1.0"
-scoreoutarg=" "
-numthreads=0
-numthreadsit=-1
-numthreadstb=-1
-randomseed=0
-addfile="/dev/null"
-addarg0=" "
-addarg=" "
-addsinglearg=" "
-add2ndhalfarg=" "
-mapoutfile="/dev/null"
-fragment=0
-legacygapopt=" "
-mergetable="/dev/null"
-mergearg=" "
-seedoffset=0
-outnum=" "
-last_e=5000
-last_m=3
-last_subopt=" "
-last_once=" "
-adjustdirection=0
-tuplesize=6
-termgapopt=" -O "
-#termgapopt=" " # gap/gap ga kakenai node
-similarityoffset="0.0"
-unalignlevel="0.0"
-unalignspecified=0
-spfactor="100.0"
-shiftpenaltyspecified=0
-opdistspecified=0
-allowshift=0
-enrich=0        # ato de kezuru
-enrichseq=0     # ato de kezuru
-enrichstr=0     # ato de kezuru
-seektarget=""   # ato de kezuru
-newdash=0
-newdash_originalsequenceonly=0
-exclude_ho=0
-fixthreshold="0.0"
-bunkatsuopt=" "
-npickup=0
-minimumweight="0.00001" # 2016/Mar
-usenaivepairscore=" "
-oldgenafparam=0
-sprigorous=0
-treeext="none"
-initialramusage="20GB"
-focusarg=" "
-lhlimit=" "
-mpiscript="/dev/null"
-if [ $# -gt 0 ]; then
-	if [ "$1" = "--version" ]; then
-		echo "$version" 1>&2
-		exit 0;
-	elif [ "$1" = "--help" -o "$1" = "--info" ]; then 
-		shift
-		er=1;
-	fi
-	while [ $# -gt 1 ];
-	do
-		if [ "$1" = "--auto" ]; then 
-			auto=1
-		elif [ "$1" = "--anysymbol" ]; then 
-			anysymbol=1
-		elif [ "$1" = "--preservecase" ]; then 
-			anysymbol=1
-		elif [ "$1" = "--clustalout" ]; then 
-			outputformat="clustal"
-		elif [ "$1" = "--phylipout" ]; then 
-			outputformat="phylip"
-		elif [ "$1" = "--reorder" ]; then 
-			outorder="aligned"
-			partorderopt=" "
-		elif [ "$1" = "--inputorder" ]; then 
-			outorder="input"
-			partorderopt=" -x "
-		elif [ "$1" = "--unweight" ]; then 
-			weightopt=" -u "
-		elif [ "$1" = "--termgappenalty" ]; then 
-			termgapopt=" "
-		elif [ "$1" = "--alga" ]; then 
-			algopt=" "
-			algoptit=" "
-#			algspecified=1
-		elif [ "$1" = "--algq" ]; then 
-			algopt=" -Q "
-			algoptit=" "
-			echo "" 1>&2
-			echo "--algq is no longer supported!" 1>&2
-			echo "" 1>&2
-			exit 1;
-#			algspecified=1
-		elif [ "$1" = "--namelength" ]; then 
-			shift   
-			namelength=`expr "$1" - 0`
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify the length of name in clustal format output!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--groupsize" ]; then 
-			shift   
-			groupsize=`expr "$1" - 0`
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify groupsize!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--partsize" ]; then 
-			shift   
-			partsize=`expr "$1" - 0`
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify partsize!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--parttree" ]; then 
-			distance="parttree"
-			partdist="ktuples"
-		elif [ "$1" = "--dpparttree" ]; then 
-			distance="parttree"
-			partdist="localalign"
-		elif [ "$1" = "--fastaparttree" ]; then 
-			distance="parttree"
-			partdist="fasta"
-		elif [ "$1" = "--treeout" ]; then 
-			treeout=1
-		elif [ "$1" = "--nodeout" ]; then 
-			nodeout=1
-			treeout=1
-		elif [ "$1" = "--distout" ]; then 
-			distout=1
-		elif [ "$1" = "--fastswpair" ]; then
-			distance="fasta"
-			pairspecified=1
-			sw=1
-		elif [ "$1" = "--fastapair" ]; then
-			distance="fasta"
-			pairspecified=1
-			sw=0
-		elif [ "$1" = "--averagelinkage" ]; then
-			treealg=" -X 1.0 "
-			sueff="1.0"
-		elif [ "$1" = "--minimumlinkage" ]; then
-			treealg=" -X 0.0 "
-			sueff="0.0"
-		elif [ "$1" = "--mixedlinkage" ]; then
-			shift   
-			sueff="$1"
-			treealg=" -X $1"
-		elif [ "$1" = "--noscore" ]; then
-			scorecalcopt=" -Z "
-		elif [ "$1" = "--6mermultipair" ]; then
-			distance="ktuplesmulti"
-			tuplesize=6
-			pairspecified=1
-		elif [ "$1" = "--10mermultipair" ]; then
-			distance="ktuplesmulti"
-			tuplesize=10
-			pairspecified=1
-		elif [ "$1" = "--6merpair" ]; then
-			distance="ktuples"
-			tuplesize=6
-			pairspecified=1
-		elif [ "$1" = "--10merpair" ]; then
-			distance="ktuples"
-			tuplesize=10
-			pairspecified=1
-		elif [ "$1" = "--blastpair" ]; then
-			distance="blast"
-			pairspecified=1
-		elif [ "$1" = "--lastmultipair" ]; then
-			distance="lastmulti"
-			pairspecified=1
-		elif [ "$1" = "--globalpair" ]; then
-			distance="global"
-			pairspecified=1
-		elif [ "$1" = "--shortlongpair" ]; then
-			distance="local"
-			usenaivepairscore="-Z"
-			laof=0.0  # addfull no tokini tsukawareru.
-			lexp=0.0  # addfull no tokini tsukawareru.
-			pgaof=0.0 # local nara iranai
-			pgexp=0.0 # local nara iranai
-			pairspecified=1
-		elif [ "$1" = "--longshortpair" ]; then
-			distance="local"
-			usenaivepairscore="-Z"
-			laof=0.0  # addfull no tokini tsukawareru.
-			lexp=0.0  # addfull no tokini tsukawareru.
-			pgaof=0.0 # local nara iranai
-			pgexp=0.0 # local nara iranai
-			pairspecified=1
-		elif [ "$1" = "--localpair" ]; then
-			distance="local"
-			pairspecified=1
-		elif [ "$1" = "--lastpair" ]; then
-			distance="last"
-			pairspecified=1
-		elif [ "$1" = "--multipair" ]; then
-			distance="multi"
-			pairspecified=1
-		elif [ "$1" = "--hybridpair" ]; then
-			distance="hybrid"
-			pairspecified=1
-		elif [ "$1" = "--scarnapair" ]; then
-			distance="scarna"
-			pairspecified=1
-		elif [ "$1" = "--dafspair" ]; then
-			distance="dafs"
-			pairspecified=1
-		elif [ "$1" = "--larapair" ]; then
-			distance="lara"
-			pairspecified=1
-		elif [ "$1" = "--slarapair" ]; then
-			distance="slara"
-			pairspecified=1
-		elif [ "$1" = "--foldalignpair" ]; then
-			distance="foldalignlocal"
-			pairspecified=1
-		elif [ "$1" = "--foldalignlocalpair" ]; then
-			distance="foldalignlocal"
-			pairspecified=1
-		elif [ "$1" = "--foldalignglobalpair" ]; then
-			distance="foldalignglobal"
-			pairspecified=1
-		elif [ "$1" = "--globalgenafpair" ]; then
-			distance="globalgenaf"
-			pairspecified=1
-			echo "" 1>&2
-			echo "--globalgenaf is no longer supported!" 1>&2
-			echo "" 1>&2
-			exit 1;
-		elif [ "$1" = "--localgenafpair" ]; then
-			distance="localgenaf"
-			pairspecified=1
-		elif [ "$1" = "--genafpair" ]; then
-			distance="localgenaf"
-			pairspecified=1
-		elif [ "$1" = "--oldgenafpair" ]; then
-			distance="localgenaf"
-			pairspecified=1
-			oldgenafparam=1
-		elif [ "$1" = "--memsave" ]; then
-			memopt=" -M -B "         # -B (bunkatsunashi no riyu ga omoidasenai)
-		elif [ "$1" = "--nomemsave" ]; then
-			memopt=" -N "
-		elif [ "$1" = "--nuc" ]; then 
-			seqtype="-D" # Deleted space, 2018/Dec
-		elif [ "$1" = "--amino" ]; then 
-			seqtype="-P" # Deleted space, 2018/Dec
-		elif [ "$1" = "--fft" ]; then 
-			fft=1
-			forcefft=1
-		elif [ "$1" = "--nofft" ]; then 
-			fft=0
-		elif [ "$1" = "--quiet" ]; then 
-#			if [ $os = "msys" ]; then
-#				progressfile="nul"
-#			else
-				progressfile="/dev/null"
-#			fi
-		elif [ "$1" = "--debug" ]; then 
-			debug=1
-		elif [ "$1" = "--coreext" ]; then 
-			coreext=" -c "
-		elif [ "$1" = "--core" ]; then 
-			coreout=1
-		elif [ "$1" = "--adjustdirection" ]; then 
-			adjustdirection=1
-		elif [ "$1" = "--adjustdirectionaccurately" ]; then 
-			adjustdirection=2
-		elif [ "$1" = "--oneiteration" ]; then 
-			oneiterationopt=" -r "
-		elif [ "$1" = "--progress" ]; then 
-			shift   
-			progressfile="$1"
-			if ! ( expr "$progressfile" : "\/" > /dev/null || expr "$progressfile" : "[A-Za-z]\:" > /dev/null ) ; then
-				echo "Specify a progress file name with the absolute path!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--out" ]; then 
-			shift   
-			outputfile="$1"
-		elif [ "$1" = "--skipanchorsremoterthan" ]; then 
-			shift   
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify maximum gap length between anchors." 1>&2
-				exit
-			fi
-			maxanchorseparation=`expr "$1" - 0` 
-		elif [ "$1" = "--anchors" ]; then 
-			shift
-			anchorfile="$1"
-			anchoropt=" -l "
-#			memopt=" -M -B "      # ato de kentou
-#			memopt=" -N "         # no memsave
-			if [ ! -e "$anchorfile" ]; then
-				echo "Cannot open $anchorfile" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--thread" ]; then 
-			shift
-			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
-				echo "Specify the number of threads.  Or, use --thread -1" 1>&2
-				exit
-			fi
-			numthreads=`expr "$1" - 0` 
-		elif [ "$1" = "--threadtb" ]; then 
-			shift
-			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
-				echo "Check the argument after --threadtb, the number of threads for the progressive step." 1>&2
-				exit
-			fi
-			numthreadstb=`expr "$1" - 0` 
-		elif [ "$1" = "--threadit" ]; then 
-			shift
-			if ! expr "$1" : "[0-9\-]" > /dev/null ; then
-				echo "Check the argument after --threadit, the number of threads for the iterative step." 1>&2
-				exit
-			fi
-			numthreadsit=`expr "$1" - 0` 
-		elif [ "$1" = "--last_subopt" ]; then 
-			last_subopt="-S"
-		elif [ "$1" = "--last_once" ]; then 
-			last_once="-U"
-		elif [ "$1" = "--last_m" ]; then 
-			shift
-			last_m=`expr "$1" - 0` 
-		elif [ "$1" = "--last_e" ]; then 
-			shift
-			last_e=`expr "$1" - 0` 
-		elif [ "$1" = "--randomseed" ]; then 
-			shift
-			randomseed=`expr "$1" - 0` 
-		elif [ "$1" = "--bestfirst" ]; then 
-			parallelizationstrategy="BESTFIRST"
-		elif [ "$1" = "--adhoc0" ]; then 
-			parallelizationstrategy="BAATARI0"
-		elif [ "$1" = "--adhoc1" ]; then 
-			parallelizationstrategy="BAATARI1"
-		elif [ "$1" = "--adhoc2" ]; then 
-			parallelizationstrategy="BAATARI2"
-		elif [ "$1" = "--simplehillclimbing" ]; then 
-			parallelizationstrategy="BAATARI2"
-		elif [ "$1" = "--scoreout" ]; then 
-			scoreoutarg="-S -B"
-		elif [ "$1" = "--outnum" ]; then 
-			outnum="-n"
-		elif [ "$1" = "--leavegappyregion" ]; then 
-			legacygapopt="-L"
-		elif [ "$1" = "--legacygappenalty" ]; then 
-			legacygapopt="-L"
-		elif [ "$1" = "--merge" ]; then
-			shift
-			mergetable="$1"
-			if [ ! -e "$mergetable" ]; then
-				echo "Cannot open $mergetable" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--addprofile" ]; then 
-			shift   
-			addarg0="-I"
-			addfile="$1"
-		elif [ "$1" = "--add" ]; then 
-			shift   
-			addarg0="-K -I"
-			addfile="$1"
-		elif [ "$1" = "--addfragments" ]; then 
-			shift   
-			addarg0="-K -I"
-			addfile="$1"
-			fragment=1
-		elif [ "$1" = "--addfull" ]; then 
-			shift   
-			addarg0="-K -I"
-			addfile="$1"
-			fragment=-1
-		elif [ "$1" = "--addlong" ]; then 
-			shift   
-			addarg0="-K -I"
-			addfile="$1"
-			fragment=-2
-		elif [ "$1" = "--smoothing" ]; then 
-			add2ndhalfarg=$add2ndhalfarg" -p "
-		elif [ "$1" = "--keeplength" ]; then 
-			add2ndhalfarg=$add2ndhalfarg" -Y "
-		elif [ "$1" = "--mapout" ]; then 
-			add2ndhalfarg=$add2ndhalfarg" -Z -Y "
-		elif [ "$1" = "--mapoutfile" ]; then 
-			shift
-			add2ndhalfarg=$add2ndhalfarg" -Z -Y "
-			mapoutfile="$1"
-		elif [ "$1" = "--maxiterate" ]; then 
-			shift   
-			iterate=`expr "$1" - 0` 
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify the number of iterations!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--retree" ]; then 
-			shift   
-			cycle=`expr "$1" - 0`
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify the number of tree rebuilding!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--aamatrix" ]; then 
-			shift   
-			f2clext="-N"
-			sbstmodel=" -b -1 "
-			scorematrix="$1"
-			if [ ! -e "$scorematrix" ]; then
-				echo "Cannot open $scorematrix" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--textmatrix" ]; then 
-			shift   
-			f2clext="-E"
-			seqtype="-P"
-			fft=0
-			sbstmodel=" -b -2 -a "
-			scorematrix="$1"
-			if [ ! -e "$scorematrix" ]; then
-				echo "Cannot open $scorematrix" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--text" ]; then 
-			f2clext="-E"
-			seqtype="-P"
-			fft=0
-			sbstmodel=" -b -2 -a "
-		elif [ "$1" = "--treein" ]; then 
-			shift   
-			treeinopt=" -U "
-			treein=1
-			treeinfile="$1"
-			if [ ! -e "$treeinfile" ]; then
-				echo "Cannot open $treeinfile" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--pileup" ]; then 
-#			treeinopt=" -U "
-#			treein=1
-			treeext="pileup"
-		elif [ "$1" = "--randomchain" ]; then 
-#			treeinopt=" -U "
-#			treein=1
-#			pileuporshuffle="s"
-			treeext="randomchain"
-		elif [ "$1" = "--topin" ]; then 
-			shift   
-			treeinopt=" -V "
-			treein=1
-			treeinfile="$1"
-			echo "The --topin option has been disabled." 1>&2
-			echo "There was a bug in version < 6.530."   1>&2
-			echo "This bug has not yet been fixed."      1>&2
-			exit 1
-		elif [ "$1" = "--mpi" ]; then 
-			mpiscript="$prefix/mpiscript"
-		elif [ "$1" = "--large" ]; then
-			treeext="memsavetree"
-		elif [ "$1" = "--memsavetree" ]; then
-			treeext="memsavetree"
-		elif [ "$1" = "--memsavetreex" ]; then
-			treeext="memsavetreex"
-		elif [ "$1" = "--stepadd" ]; then
-			treeext="stepadd"
-		elif [ "$1" = "--youngestlinkage" ]; then
-			treeext="youngestlinkage"
-		elif [ "$1" = "--kappa" ]; then 
-			shift   
-			kappa=" -k $1 "
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify kappa value!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--fmodel" ]; then 
-			fmodel=" -a "
-		elif [ "$1" = "--nwildcard" ]; then 
-			nmodel=" -: "
-		elif [ "$1" = "--nzero" ]; then 
-			nmodel="  "
-		elif [ "$1" = "--jtt" ]; then 
-			shift   
-			f2clext="-N"
-			sbstmodel=" -j $1"
-#			if ! expr "$1" : "[0-9]" > /dev/null ; then
-#				echo "Specify pam value!" 1>&2
-#				exit
-#			fi
-		elif [ "$1" = "--kimura" ]; then 
-			shift   
-			f2clext="-N"
-			sbstmodel=" -j $1"
-#			if ! expr "$1" : "[0-9]" > /dev/null ; then
-#				echo "Specify pam value!" 1>&2
-#				exit
-#			fi
-		elif [ "$1" = "--tm" ]; then 
-			shift   
-			f2clext="-N"
-			sbstmodel=" -m $1"
-#			if ! expr "$1" : "[0-9]" > /dev/null ; then
-#				echo "Specify pam value!" 1>&2
-#				exit
-#			fi
-		elif [ "$1" = "--bl" ]; then 
-			shift   
-			f2clext="-N"
-			sbstmodel=" -b $1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "blosum $1?" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--weighti" ]; then
-			shift   
-			weighti="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify weighti value!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--weightr" ]; then
-			shift   
-			weightr="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify weightr value!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--weightm" ]; then
-			shift   
-			weightm="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify weightm value!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--rnaalifold" ]; then
-			rnaalifold=1
-		elif [ "$1" = "--mccaskill" ]; then
-			mccaskill=1
-			contrafold=0
-			dafs=0
-		elif [ "$1" = "--contrafold" ]; then
-			mccaskill=0
-			contrafold=1
-			dafs=0
-		elif [ "$1" = "--dafs" ]; then
-			mccaskill=0
-			contrafold=0
-			dafs=1
-		elif [ "$1" = "--ribosum" ]; then
-			rnascoremtx=" -s "
-		elif [ "$1" = "--op" ]; then 
-			shift   
-			gop="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify op!" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--opdist" ]; then 
-			shift   
-			gopdist="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify opdist!" 1>&2
-				exit
-			fi
-			opdistspecified=1
-		elif [ "$1" = "--allowshift" ]; then 
-			allowshift=1
-		elif [ "$1" = "--shiftpenalty" ]; then 
-			shift   
-			spfactor="$1"
-			if ! expr "$1" : "[0-9]" > /dev/null ; then
-				echo "Specify sf!" 1>&2
-				exit
-			fi
-			shiftpenaltyspecified=1
-		elif [ "$1" = "--exp" ]; then 
-			shift   
-#			gexp="$1"
-			tmpval="$1"
-			gexp=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
-			if ! expr "$gexp" : "[0-9\-]" > /dev/null ; then
-				printf "\nSpecify a number for exp, like --exp 0.1\n" 1>&2
-				printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--ep" ]; then 
-			shift   
-#			aof="$1"
-			tmpval="$1"
-			aof=`awk "BEGIN{ print -1.0 * \"$tmpval\"}"`
-			if ! expr "$aof" : "[0-9\-]" > /dev/null ; then
-				printf "\nSpecify a number for ep, like --ep 0.1\n" 1>&2
-				printf "'$1' cannot be interpreted as a number..\n\n" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--rop" ]; then 
-			shift   
-			rgop="$1"
-# Atode check
-		elif [ "$1" = "--rep" ]; then 
-			shift   
-			rgep="$1"
-		elif [ "$1" = "--lop" ]; then 
-			shift   
-			lgop="$1"
-		elif [ "$1" = "--LOP" ]; then 
-			shift   
-			LGOP="$1"
-		elif [ "$1" = "--lep" ]; then 
-			shift   
-			laof="$1"
-		elif [ "$1" = "--lexp" ]; then 
-			shift   
-			lexp="$1"
-		elif [ "$1" = "--LEXP" ]; then 
-			shift   
-			LEXP="$1"
-		elif [ "$1" = "--GEXP" ]; then 
-			shift   
-			GEXP="$1"
-		elif [ "$1" = "--GOP" ]; then 
-			shift   
-			GGOP="$1"
-		elif [ "$1" = "--gop" ]; then 
-			shift   
-			pggop="$1"
-		elif [ "$1" = "--gep" ]; then 
-			shift   
-			pgaof="$1"
-		elif [ "$1" = "--gexp" ]; then 
-			shift   
-			pgexp="$1"
-		elif [ "$1" = "--laraparams" ]; then 
-			shift   
-			laraparams="$1"
-		elif [ "$1" = "--corethr" ]; then 
-			shift   
-			corethr="$1"
-		elif [ "$1" = "--corewin" ]; then 
-			shift   
-			corewin="$1"
-		elif [ "$1" = "--strdir" ]; then
-			shift
-			strdir="$1"
-		elif [ "$1" = "--pdbidlist" ]; then
-			echo "--pdbidlist is temporarily unavailable, 2018/Dec." 1>&2
-			echo "" 1>&2
-			exit
-			shift
-			pdblist="$1"
-			if [ ! -e "$pdblist" ]; then
-				echo "Cannot open $pdblist" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-		elif [ "$1" = "--pdbfilelist" ]; then
-			echo "--pdbfilelist is temporarily unavailable, 2018/Dec." 1>&2
-			echo "" 1>&2
-			exit
-			shift
-			ownlist="$1"
-			if [ ! -e "$ownlist" ]; then
-				echo "Cannot open $ownlist" 1>&2
-				echo "" 1>&2
-				exit
-			fi
-#		elif [ "$1" = "--enrich" ]; then
-#			enrich=1
-#			enrichseq=1
-#			enrichstr=1
-#			seektarget=""
-#		elif [ "$1" = "--enrichseq" ]; then
-#			enrich=1
-#			enrichseq=1
-#			enrichstr=0
-#			seektarget="-seq"
-#		elif [ "$1" = "--enrichstr" ]; then
-#			enrich=1
-#			enrichseq=0
-#			enrichstr=1
-#			seektarget="-str"
-		elif [ "$1" = "--dash" ]; then
-			newdash=1
-			distance="global" # can be override
-			iterate=3         # can be override
-		elif [ "$1" = "--originalseqonly" ]; then
-			newdash_originalsequenceonly=1
-		elif [ "$1" = "--excludehomologs" ]; then # works with --dash only
-			exclude_ho=1
-		elif [ "$1" = "--seedtable" ]; then
-			shift
-			seedtable="y"
-			seedtablefile="$1"
-		elif [ "$1" = "--seed" ]; then
-			shift
-			seed="m"
-			seedfiles="$seedfiles $1"
-		elif [ "$1" = "--minimumweight" ]; then
-			shift
-			minimumweight="$1"
-		elif [ "$1" = "--similaritylevel" ]; then
-			shift
-			similarityoffset="$1"
-		elif [ "$1" = "--unalignlevel" ]; then
-			shift
-			unalignlevel="$1"
-			unalignspecified=1
-		elif [ "$1" = "--skipiterate" ]; then
-			shift
-			fixthreshold="$1"
-		elif [ "$1" = "--bunkatsunashi" ]; then
-			bunkatsuopt=" -B "
-		elif [ "$1" = "--sp" ]; then
-			sprigorous=1
-		elif [ "$1" = "--focus" ]; then
-			focusarg=" -= "
-		elif [ "$1" = "--lhlimit" ]; then # atode namae henkou
-			shift
-			lhlimit=" -q $1 "
-		elif [ "$1" = "--sparsepickup" ]; then
-			shift
-			npickup="$1"
-		elif [ $progname = "fftns" -o  $progname = "nwns" ]; then
-			if [ "$1" -gt 0 ]; then
-				cycle=`expr "$1" - 0`
-			fi
-		else
-			echo "Unknown option:  $1" 1>&2
-			er=1;
-#			exit 1;
-		fi
-		shift   
-	done;
-
-
-#	echo "" 1>"$progressfile"
-
-	if [ $treeext = "memsavetree" ] || [ $treeext = "stepadd" ]; then
-		if [ $distance != "ktuples" ]; then  
-# auto -> memsave && globalpair ha erabarenai node, 
-# ~/maffttmp wo tsukau noha meijiteki ni shitei saretatoki dake.
-			if [ ! "$MAFFT_TMPDIR" ]; then  # space is acceptable, 2018/Mar/17
-				MAFFT_TMPDIR="$HOME/maffttmp"
-				mkdir -p "$MAFFT_TMPDIR" || exit
-			fi
-		fi
-	fi
-
-
-	if [ ! "$MAFFT_TMPDIR" ]; then
-		MAFFT_TMPDIR="$TMPDIR"
-	fi
-
-	TMPFILE=`env TMPDIR="$MAFFT_TMPDIR" mktemp -dt "$progname.XXXXXXXXXX"`
-	if [ $? -ne 0 ]; then
-		echo "mktemp seems to be obsolete. Re-trying without -t" 1>&2
-		mkdir -p "$MAFFT_TMPDIR/tmp" 1>&2
-		TMPFILE=`mktemp -d "$MAFFT_TMPDIR/tmp/$progname.XXXXXXXXXX"`
-	fi	
-
-#	lfs getstripe $TMPFILE  2>/dev/null && lfs setstripe -c 1 $TMPFILE # 2017/Oct
-	lfs getstripe "$TMPFILE" > /dev/null 2>&1 && lfs setstripe -c 1 "$TMPFILE" > /dev/null 2>&1 # 2018/Feb
-
-	if [ $os = "cygwin" ]; then
-		TMPFILE=`cygpath -w "$TMPFILE"`  # necessary to pass path to f2cl on cyswin, somehow unnecessary in msys.
-	fi
-
-	umask 077
-#	mkdir  "$TMPFILE"  || er=1
-
-
-function removetmpfile() { # for MPI
-	while true
-	do
-		rm -rf "$TMPFILE" && break
-		echo Retrying to remove "$TMPFILE". It may take several seconds. 1>&2
-		sleep 2
-	done
-}
-
-	if [ $debug -eq 1 ]; then
-#		trap "tar cfvz debuginfo.tgz $TMPFILE; rm -rf $TMPFILE " 0 # does not work in msys
-#		trap "tar cfv - $TMPFILE | gzip -c > debuginfo.tgz; rm -rf $TMPFILE " 0 15
-		trap "tar cfv - \"$TMPFILE\" | gzip -c > debuginfo.tgz; removetmpfile" 0 15
-	else
-#		trap "rm -rf $TMPFILE" 0 15
-		trap "removetmpfile" 0 15
-	fi
-	if [ $# -eq 1 ]; then
-		if [ -r "$1" -o "$1" = - ]; then
-
-			if [ -r "$addfile" ]; then
-				printf '';
-			else
-				echo "$0": Cannot open "$addfile". 1>&2
-				echo "" 1>&2
-				exit 1;
-			fi
-
-
-			cat "$1"              | tr "\r" "\n" > "$TMPFILE/infile"
-			echo ""                             >> "$TMPFILE/infile"
-			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" >> "$TMPFILE/infile"
-			cat "$addfile"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_addfile"
-			cat "$scorematrix"    | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_aamtx"
-			cat "$mergetable"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_subalignmentstable"
-			cat "$treeinfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_guidetree"
-			cat "$seedtablefile"  | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_seedtablefile"
-			cat "$laraparams"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_lara.params"
-			cat "$pdblist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/pdblist"
-			cat "$ownlist"        | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/ownlist"
-			cat "$anchorfile"     | tr "\r" "\n" | grep -v "^$" > "$TMPFILE/_externalanchors"
-
-			SAVEIFS=$IFS
-			IFS='\n'
-			filelist="$1\n$addfile\n$scorematrix\n$mergetable\n$treeinfile\n$seedtablefile\n$laraparams\n$pdblist\n$ownlist"
-			for f in $filelist; do
-				# $f="" demo mudani file ga hashiru.
-				file "$f" 2>/dev/null | grep "UTF-[13][62]" >& /dev/null && printf "$f: UTF-16 or UTF-32? Convert this file to ASCII\n\n" 1>&2 && exit 1;
-			done
-			IFS=$SAVEIFS
-
-#			echo $seedfiles
-			infilename="$1"
-			seedfilesintmp="/dev/null"
-			seednseq="0"
-			set $seedfiles > /dev/null
-			while [ $# -gt 1 ];
-			do
-				shift
-				if [ -r "$1" ]; then
-					cat "$1" | tr "\r" "\n" >  "$TMPFILE/seed$#"
-					file "$1" | grep "UTF-[13][62]" >& /dev/null && printf "$1: UTF-16 or UTF-32?  Convert this file to ASCII\n\n" 1>&2 && exit 1;
-				else
-					echo "$0": Cannot open "$1". 1>&2
-					echo "" 1>&2
-					exit 1;
-				fi
-				seednseq=$seednseq" "`grep -c '^[>|=]' "$TMPFILE/seed$#"`
-				seedfilesintmp=$seedfilesintmp" "seed$#
-			done
-#			ls $TMPFILE
-#			echo $seedfilesintmp
-#			echo $seednseq
-
-
-		else
-			echo "$0": Cannot open "$1". 1>&2
-			echo "" 1>&2
-			er=1
-#			exit 1;
-		fi
-	else
-#		echo '$#'"=$#" 1>&2
-		er=1
-	fi
-
-
-	if [ $numthreads -lt 0 ]; then
-		if [ $os = "linux" ]; then
-			nlogicalcore=`cat /proc/cpuinfo | grep "^processor" | uniq | wc -l`
-			ncoresinacpu=`cat /proc/cpuinfo | grep 'cpu cores' | uniq | awk '{print $4}'`
-			nphysicalcpu=`cat /proc/cpuinfo | grep 'physical id' | sort | uniq | wc -l`
-			if [ $nlogicalcore -eq 0 ]; then
-				echo "Cannot get the number of processors from /proc/cpuinfo" 1>>"$progressfile"
-				exit 1
-			fi
-			if [ ${#ncoresinacpu} -gt 0 -a $nphysicalcpu -gt 0 ]; then
-				numthreads=`expr $ncoresinacpu '*' $nphysicalcpu`
-#				if [ $nlogicalcore -gt $numthreads ]; then    # Hyperthreading
-#					numthreads=`expr $numthreads '+' 1`
-#				fi
-			else
-				numthreads=$nlogicalcore
-			fi
-		elif [ $os = "darwin" ]; then
-			numthreads=`sysctl -n hw.physicalcpu`
-			if [ -z $numthreads ]; then
-				echo "Cannot get the number of physical cores from sysctl" 1>>"$progressfile"
-				exit 1
-			fi
-#			nlogicalcore=`sysctl -n hw.logicalcpu`
-#			if [ $nlogicalcore -gt $numthreads ]; then    # Hyperthreading
-#				numthreads=`expr $numthreads '+' 1`
-#			fi
-		elif [ "$windows" = "yes" ]; then
-#			numthreads=`wmic cpu get NumberOfCores | head -2 | tail -1 | awk '{print $1}'`
-			numthreads=`wmic cpu get NumberOfCores | awk 'BEGIN{n=0} {n+=$1} END{print n}'`
-
-		else
-			echo "Cannot count the number of physical cores." 1>>"$progressfile"
-			exit 1
-		fi
-		echo "OS = "$os 1>>"$progressfile"
-		echo "The number of physical cores = " $numthreads 1>>"$progressfile"
-	fi
-
-	if [ $numthreadstb -lt 0 ]; then
-		if [ $numthreads -lt 16 -o "$mpiscript" !=  "/dev/null" ]; then # mpi: museigen, multithread: 16 made
-#		if [ $numthreads -lt 31 ]; then
-			numthreadstb=$numthreads
-		else
-			numthreadstb=16
-		fi
-	fi
-
-	if [ $numthreadsit -lt 0 ]; then
-		if [ $numthreads -lt 8 ]; then
-			numthreadsit=$numthreads
-		else
-			numthreadsit=8
-		fi
-	fi
-
-	if [ $numthreadsit -eq 0 -a $parallelizationstrategy = "BESTFIRST" ]; then
-		echo 'Impossible' 1>&2;
-		exit 1;
-	fi
-
-	if [ "$addarg0" != " " ]; then
-#		iterate=0  # 2013/03/23 -> commented out, 2017/12
-		"$prefix/countlen" < "$TMPFILE/_addfile" > "$TMPFILE/addsize" 2>>"$progressfile"
-		nadd=`awk '{print $1}' "$TMPFILE/addsize"`
-		if [ $nadd -eq "0" ]; then
-			echo Check $addfile 1>&2
-			exit 1;
-		fi
-		if [ $seed != "x" -o $seedtable != "x" ]; then
-			echo 'Impossible' 1>&2;
-			echo 'Use either ONE of --seed, --seedtable, --addprofile and --add.' 1>&2
-			exit 1;
-		fi
-	else
-		nadd="0"
-	fi
-
-	if [ $auto -eq 1 ]; then
-		"$prefix/countlen" < "$TMPFILE/infile" > "$TMPFILE/size" 2>>"$progressfile"
-		nseq=`awk '{print $1}' "$TMPFILE/size"`
-		nlen=`awk '{print $3}' "$TMPFILE/size"`
-
-		if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
-			distance="local"
-			iterate=1000
-			cycle=1
-			treeext="none"
-		elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
-			distance="local"
-			iterate=2
-			cycle=1
-			treeext="none"
-		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
-			distance="ktuples"
-			iterate=2
-			cycle=2
-			treeext="none"
-		elif [ $nseq -lt 20000 ]; then  # changed from 10000 2014/Oct/4
-			distance="ktuples"
-			iterate=0
-			cycle=2
-			treeext="none"
-		elif [ $nseq -lt 100000 ]; then  # changed from 50000 2017/Nov/24
-			distance="ktuples"
-			iterate=0
-			cycle=2
-			if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
-				treeext="memsavetree"
-			fi
-		elif [ $nseq -lt 200000 ]; then  # changed from 90000 2017/Nov/24
-			distance="ktuples"
-			iterate=0
-			cycle=1
-			if [ $fragment -eq 0 -a "$mergetable" = "/dev/null" ]; then
-				treeext="memsavetree"
-			fi
-		elif [ $nlen -lt 3000 ]; then
-			distance="parttree"
-			partdist="localalign"
-			algopt=" "
-			algoptit=" "
-#			algspecified=1
-			cycle=1
-		else
-			distance="parttree"
-			partdist="ktuples"
-			algopt=" "
-			algoptit=" "
-#			algspecified=1
-			cycle=1
-		fi
-
-
-#		if [ $nlen -lt 3000 -a $nseq -lt 100 ]; then
-#			distance="local"
-#			iterate=1000
-#			cycle=1
-#		elif [ $nlen -lt 1000 -a $nseq -lt 200 ]; then
-#			distance="local"
-#			iterate=2
-#			cycle=1
-#		elif [ $nlen -lt 10000 -a $nseq -lt 500 ]; then
-#			distance="ktuples"
-#			iterate=2
-#			cycle=2
-#		elif [ $nseq -lt 200000 ]; then
-#			distance="ktuples"
-#			iterate=0
-#			treeinopt=" -U "
-#			treein=1
-#			pileuporshuffle="a"
-#		elif [ $nlen -lt 3000 ]; then
-#			distance="parttree"
-#			partdist="localalign"
-#			algopt=" "
-#			algoptit=" "
-##			algspecified=1
-#			cycle=1
-#		else
-#			distance="parttree"
-#			partdist="ktuples"
-#			algopt=" "
-#			algoptit=" "
-##			algspecified=1
-#			cycle=1
-#		fi
-
-
-		if [ $fragment -ne 0 ]; then
-			norg=`expr $nseq '-' $nadd`
-			npair=`expr $norg '*' $nadd`
-			echo "nadd = " $nadd               1>>"$progressfile"
-			echo "npair = " $npair             1>>"$progressfile"
-			echo "nseq = " $nseq               1>>"$progressfile"
-			echo "nlen = " $nlen               1>>"$progressfile"
-# nagasa check!
-#
-			if [ $npair -gt 10000000 -o $nlen -gt 5000 ]; then  # 2017/Oct 
-				distance="ktuples"
-				echo "use ktuples, size=$tuplesize!" 1>>"$progressfile"
-			elif [ $npair -gt 3000000 -o $nlen -gt 5000 ]; then  # 2017/Oct
-				distance="multi"
-				weighti="0.0"
-				echo "use multipair, weighti=0.0!" 1>>"$progressfile"
-			else
-				distance="multi"
-				echo "use multipair, weighti=$weighti!" 1>>"$progressfile"
-			fi
-			pairspecified=1
-		fi
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$sueff\" < 0.0 || 0.0+\"$sueff\" > 1.0 )}"` -gt 0 ]; then
-		printf "\n%s\n\n" "The argument of --mixedlinkage must be between 0.0 and 1.0" 1>>"$progressfile"
-		exit 1;
-	fi
-
-	if [ $allowshift -eq 1 ]; then
-		if [ $unalignspecified -ne 1 ]; then
-			unalignlevel="0.8"
-		fi
-		if [ $shiftpenaltyspecified -ne 1 ]; then
-			spfactor="2.00"
-		fi
-	fi
-
-	if [ $opdistspecified -ne 1 ]; then
-		gopdist=$gop
-	fi
-
-	if [ $unalignlevel != "0.0" -o `awk "BEGIN {print( 0.0+\"$spfactor\" < 100.0 )}"` -gt 0 ]; then
-		nmodel=" -: "
-		termgapopt=" "
-		if [ $distance = "localgenaf" ]; then
-			printf "\n%s\n" "The combination of --allowshift and --genafpair (E-INS-i/-1) is not supported." 1>>"$progressfile"
-			printf "%s\n" "Instead, please try --allowshift --globalpair (G-INS-i/-1 in the web version)," 1>>"$progressfile"
-			printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i/-1), too." 1>>"$progressfile"
-			exit 1;
-		fi
-		if [ $distance != "global" -o `awk "BEGIN {print( 0.0+\"$weighti\" < 1.0 )}"` -gt 0 ]; then
-			printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is supported only with the --globalpair option." 1>>"$progressfile"
-			exit 1;
-		fi
-		if [ $fragment -ne 0 ]; then
-			printf "\n%s\n\n" "At present, --unalignlevel # or --allowshift is not supported with the --addfragments option." 1>>"$progressfile"
-			exit 1;
-		fi
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$spfactor\" < 1.0 )}"` -gt 0 ]; then
-			printf "\n%s\n" "shiftpenalty must be >1." 1>>"$progressfile"
-			exit 1;
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$fixthreshold\" < 0.0 )}"` -gt 0 ]; then
-		printf "\n%s\n\n" "The 'fix' parameter must be >= 0.0" 1>>"$progressfile"
-		exit 1;
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" < 0.0 || 0.0+\"$unalignlevel\" > 1.0 )}"` -gt 0 ]; then
-		printf "\n%s\n\n" "The 'unalignlevel' parameter must be between 0.0 and 1.0" 1>>"$progressfile"
-		exit 1;
-	fi
-	if [ `awk "BEGIN {print( 0.0+\"$unalignlevel\" > 0.0 )}"` -gt 0 ]; then
-		laof="0"
-		lexp="0"
-		pgaof="0"
-		pgexp="0"
-		LEXP="0"
-		GEXP="0"
-		termgapopt=" "
-#		if [ $auto -eq 1 -o $fragment -ne 0 -o $iterate -gt 0 ]; then
-		if [ $fragment -ne 0 ]; then
-			printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported with the --addfragments option." 1>>"$progressfile"
-			exit 1;
-		fi
-		if [ $distance = "parttree" ]; then
-			printf "\n%s\n\n" "At present, the 'unalignlevel > 0' mode is not supported in the (dp)parttree option." 1>>"$progressfile"
-			exit 1;
-		fi
-		if [ $distance = "localgenaf" ]; then
-			printf "\n%s\n" "The --genafpair is not supported in the 'unalignlevel > 0' mode." 1>>"$progressfile"
-			printf "%s\n" "Instead, please try --unalignlevel xx --globalpair," 1>>"$progressfile"
-			printf "%s\n\n" "which covers the situation for --genafpair (E-INS-i), too." 1>>"$progressfile"
-			exit 1;
-		fi
-#		if [ $distance != "ktuples" -a `awk "BEGIN {print( 0.0+\"$weighti\" > 0.0 )}"` -gt 0 -a $iterate -gt 0 ]; then
-#			printf "\n%s\n\n" "Please add --weighti 0.0, for now." 1>>"$progressfile"
-#			exit 1;
-#		fi
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" != 0.0 && 0.0+\"$unalignlevel\" != 0.0 )}"` -gt 0 ]; then
-		printf "\n%s\n\n" "Do not simultaneously specify --similaritylevel and --unalignlevel" 1>>"$progressfile"
-		exit 1;
-	fi
-
-	if [ `awk "BEGIN {print( 0.0+\"$similarityoffset\" < -1.0 || 0.0+\"$similarityoffset\" > 1.0 )}"` -gt 0 ]; then
-		printf "\n%s\n\n" "Similarity must be between -1.0 and +1.0" 1>>"$progressfile"
-		exit 1;
-	fi
-	aof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $aof}"`
-	laof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $laof}"`
-	pgaof=`awk "BEGIN{print 0.0 + \"$similarityoffset\" + $pgaof}"`
-
-
-	if [ $parallelizationstrategy = "BESTFIRST" -o  $parallelizationstrategy = "BAATARI0" ]; then
-		iteratelimit=254
-	else
-		iteratelimit=16
-	fi
-	if [ $iterate -gt $iteratelimit ]; then    #??
-		iterate=$iteratelimit
-	fi
-
-	if [ $rnaalifold -eq 1 ]; then
-		rnaopt=" -e $rgep -o $rgop -c $weightm -r $weightr -R $rnascoremtx "
-#		rnaoptit=" -o $rgop -BT -c $weightm -r $weightr -R "
-		rnaoptit=" -o $rgop -F -c $weightm -r $weightr -R "
-	elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $contrafold -eq 1 ]; then
-		rnaopt=" -o $rgop -c $weightm -r $weightr "
-#		rnaoptit=" -e $rgep -o $rgop -BT -c $weightm -r $weightr $rnascoremtx "
-		rnaoptit=" -e $rgep -o $rgop -F -c $weightm -r $weightr $rnascoremtx "
-	else
-		rnaopt="  "
-		rnaoptit=" -F "
-	fi
-
-#	if [ $algspecified -eq 0 ]; then
-#		if [ $distance = "parttree" ]; then 
-#			algopt=" -Q "
-#			algoptit=" "
-#		else
-#			algopt=" "
-#			algoptit=" "
-#		fi
-#	fi
-
-	if [ $sprigorous -eq 1 ]; then
-		algopt=" -@ "
-		if [ $iterate -gt 0 ]; then
-			if [ $numthreadsit -eq 0 ]; then
-				algoptit=" -@ -B -Z -z 1000 "
-			else
-				echo "" 1>>"$progressfile"
-				echo "At present, the combination of --sp and iterative refinement is supported only in a single thread." 1>>"$progressfile"
-				echo "Please try \"--thread -1 --threadit 0\", which runs the iterative refinment calculation on a single thread." 1>>"$progressfile"
-				echo "" 1>>"$progressfile"
-				exit 1;
-#				algoptit=" -@ -B -z 1000 "
-			fi
-		fi
-		termgapopt=" "
-		fft=0
-		memopt=" -N "
-	fi
-
-	model="$sbstmodel $kappa $fmodel $nmodel"
-
-	if [ $er -eq 1 ]; then
-		echo "------------------------------------------------------------------------------" 1>&2
-		echo "  MAFFT" $version 1>&2
-#		echo "" 1>&2
-#		echo "  Input format: fasta" 1>&2
-#		echo ""  1>&2
-#		echo "  Usage: `basename $0` [options] inputfile > outputfile" 1>&2
-	    echo "  https://mafft.cbrc.jp/alignment/software/" 1>&2
-		echo "  MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)"        1>&2
-#		echo "------------------------------------------------------------------------------" 1>&2
-#		echo "  % mafft in > out" 1>&2
-		echo "------------------------------------------------------------------------------" 1>&2
-#		echo ""  1>&2
-		echo "High speed:" 1>&2
-		echo "  % mafft in > out" 1>&2
-		echo "  % mafft --retree 1 in > out (fast)" 1>&2
-		echo "" 1>&2
-		echo "High accuracy (for <~200 sequences x <~2,000 aa/nt):" 1>&2
-		echo "  % mafft --maxiterate 1000 --localpair  in > out (% linsi in > out is also ok)" 1>&2
-		echo "  % mafft --maxiterate 1000 --genafpair  in > out (% einsi in > out)" 1>&2
-		echo "  % mafft --maxiterate 1000 --globalpair in > out (% ginsi in > out)" 1>&2
-		echo "" 1>&2
-		echo "If unsure which option to use:" 1>&2
-		echo "  % mafft --auto in > out" 1>&2
-		echo "" 1>&2
-#		echo "Other options:" 1>&2
-		echo "--op # :         Gap opening penalty, default: 1.53" 1>&2
-		echo "--ep # :         Offset (works like gap extension penalty), default: 0.0" 1>&2
-		echo "--maxiterate # : Maximum number of iterative refinement, default: 0" 1>&2
-		echo "--clustalout :   Output: clustal format, default: fasta" 1>&2
-		echo "--reorder :      Outorder: aligned, default: input order" 1>&2
-		echo "--quiet :        Do not report progress" 1>&2
-		echo "--thread # :     Number of threads (if unsure, --thread -1)" 1>&2
-		echo "--dash :         Add structural information (Rozewicki et al, submitted)" 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --localpair in > out (L-INS-i)" 1>&2
-#		echo " most accurate in many cases, assumes only one alignable domain" 1>&2 
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --genafpair in > out (E-INS-i)" 1>&2
-#		echo " works well if many unalignable residues exist between alignable domains" 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 --globalpair in > out (G-INS-i)" 1>&2
-#		echo " suitable for globally alignable sequences            " 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --maxiterate 1000 in > out (FFT-NS-i)" 1>&2
-#		echo " accurate and slow, iterative refinement method      " 1>&2
-#		echo "" 1>&2
-#		echo "If the input sequences are long (~1,000,000nt)," 1>&2
-#		echo " % mafft --retree 1 --memsave --fft in > out (FFT-NS-1-memsave, new in v5.8)" 1>&2
-#		echo "" 1>&2
-#		echo "If many (~5,000) sequences are to be aligned," 1>&2
-#		echo "" 1>&2
-#		echo " % mafft --retree 1 [--memsave] --nofft in > out (NW-NS-1, new in v5.8)" 1>&2
-#		echo "" 1>&2
-#		echo " --localpair :      All pairwise local alignment information is included"  1>&2
-#		echo "                    to the objective function, default: off"  1>&2
-#		echo " --globalpair :     All pairwise global alignment information is included"  1>&2
-#		echo "                    to the objective function, default: off"  1>&2
-#		echo " --op # :           Gap opening penalty, default: $defaultgop " 1>&2
-#		echo " --ep # :           Offset (works like gap extension penalty), default: $defaultaof " 1>&2
-#		echo " --bl #, --jtt # :  Scoring matrix, default: BLOSUM62" 1>&2
-#		echo "                    Alternatives are BLOSUM (--bl) 30, 45, 62, 80, " 1>&2
-#		echo "                    or JTT (--jtt) # PAM. " 1>&2
-#		echo " --nuc or --amino : Sequence type, default: auto" 1>&2
-#		echo " --retree # :       The number of tree building in progressive method " 1>&2
-#		echo "                    (see the paper for detail), default: $defaultcycle " 1>&2
-#		echo " --maxiterate # :   Maximum number of iterative refinement, default: $defaultiterate " 1>&2
-#		if [ $defaultfft -eq 1 ]; then
-#			echo " --fft or --nofft:  FFT is enabled or disabled, default: enabled" 1>&2
-#		else
-#			echo " --fft or --nofft:  FFT is enabled or disabled, default: disabled" 1>&2
-#		fi
-#		echo " --memsave:         Memory saving mode" 1>&2
-#		echo "                    (for long genomic sequences), default: off" 1>&2
-#		echo " --clustalout :     Output: clustal format, default: fasta" 1>&2
-#		echo " --reorder :        Outorder: aligned, default: input order" 1>&2
-#		echo " --quiet :          Do not report progress" 1>&2
-#		echo "-----------------------------------------------------------------------------" 1>&2
-		exit 1; 
-	fi
-	if [ $sw -eq 1 ]; then
-		swopt=" -A "
-	else
-		swopt=" "
-	fi
-
-	if [ $distance = "fasta" -o $partdist = "fasta" ]; then
-		if [ ! "$FASTA_4_MAFFT" ]; then
-			FASTA_4_MAFFT=`which fasta34`
-		fi
-
-		if [ ! -x "$FASTA_4_MAFFT" ]; then
-			echo ""       1>&2
-			echo "== Install FASTA ========================================================" 1>&2
-			echo "This option requires the fasta34 program (FASTA version x.xx or higher)"   1>&2
-			echo "installed in your PATH.  If you have the fasta34 program but have renamed" 1>&2
-			echo "(like /usr/local/bin/myfasta), set the FASTA_4_MAFFT environment variable" 1>&2
-			echo "to point your fasta34 (like setenv FASTA_4_MAFFT /usr/local/bin/myfasta)." 1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "last" -o $distance = "lastmulti" ]; then
-		if [ ! -x "$prefix/lastal" -o ! -x "$prefix/lastdb" ]; then
-			echo ""       1>&2
-			echo "== Install LAST ============================================================" 1>&2
-			echo "LAST (Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487) is required." 1>&2
-			echo "http://last.cbrc.jp/"                                                       1>&2
-			echo "http://mafft.cbrc.jp/alignment/software/xxxxxxx.html "                      1>&2
-			echo "============================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "lara" -o $distance = "slara" ]; then
-		if [ ! -x "$prefix/mafft_lara" ]; then
-			echo ""       1>&2
-			echo "== Install LaRA =========================================================" 1>&2
-			echo "This option requires LaRA (Bauer et al. http://www.planet-lisa.net/)."     1>&2
-			echo "The executable have to be renamed to 'mafft_lara' and installed into "     1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "A configuration file of LaRA also have to be given"                        1>&2
-			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
-			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-		if [ ! -s "$laraparams" ]; then
-			echo ""       1>&2
-			echo "== Configure LaRA =======================================================" 1>&2
-			echo "A configuration file of LaRA have to be given"                             1>&2
-			echo "mafft-xinsi --larapair --laraparams parameter_file"                        1>&2
-			echo "mafft-xinsi --slarapair --laraparams parameter_file"                       1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
-	if [ ! -x "$prefix/foldalign210" ]; then
-			echo ""       1>&2
-			echo "== Install FOLDALIGN ====================================================" 1>&2
-			echo "This option requires FOLDALIGN (Havgaard et al. http://foldalign.ku.dk/)." 1>&2
-			echo "The executable have to be renamed to 'foldalign210' and installed into "   1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "scarna" -o $mccaskill -eq 1 ]; then
-		if [ ! -x "$prefix/mxscarnamod" ]; then
-			echo ""       1>&2
-			echo "== Install MXSCARNA ======================================================" 1>&2
-			echo "MXSCARNA (Tabei et al. BMC Bioinformatics 2008 9:33) is required."          1>&2
-			echo "Please 'make' at the 'extensions' directory of the MAFFT source package,"   1>&2
-			echo "which contains the modified version of MXSCARNA."                           1>&2
-			echo "http://mafft.cbrc.jp/alignment/software/source.html "                1>&2
-			echo "==========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $distance = "dafs" -o $dafs -eq 1 ]; then
-		if [ ! -x "$prefix/dafs" ]; then
-			echo ""       1>&2
-			echo "== Install DAFS===========================================================" 1>&2
-			echo "DAFS (Sato et al. Journal 2012 issue:page) is required."                    1>&2
-			echo "http://www.ncrna.org/ "                                                     1>&2
-			echo "==========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-	if [ $contrafold -eq 1 ]; then
-		if [ ! -x "$prefix/contrafold" ]; then
-			echo ""       1>&2
-			echo "== Install CONTRAfold ===================================================" 1>&2
-			echo "This option requires CONTRAfold"                                           1>&2
-			echo "(Do et al. http://contra.stanford.edu/contrafold/)."                       1>&2
-			echo "The executable 'contrafold' have to be installed into "                    1>&2
-			echo "the $prefix directory. "                                                   1>&2
-			echo "=========================================================================" 1>&2
-			echo "" 1>&2
-			exit 1
-		fi
-	fi
-
-#old
-#	if [ $treeout -eq 1 ]; then
-#		parttreeoutopt="-t"
-#		if [ $cycle -eq 0 ]; then
-#			treeoutopt="-t -T"
-#			groupsize=1
-#			iterate=0 
-#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-#				distance="distonly"
-#			fi
-#		else
-#			treeoutopt="-t"
-#		fi
-#	else
-#		parttreeoutopt=" "
-#		if [ $cycle -eq 0 ]; then
-#			treeoutopt="-t -T"
-#			iterate=0 
-#			if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-#				distance="distonly"
-#			fi
-#		else
-#			treeoutopt=" "
-#		fi
-#	fi
-
-#new
-	if [ $cycle -eq 0 ]; then
-		if [ $nodeout -eq 1 ]; then
-			treeoutopt="-^ -T"
-		else
-			treeoutopt="-t -T"
-		fi
-		iterate=0 
-		weighti="0.0"  # 2016Jul31, tbfast.c kara idou
-#		if [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o $distance = "globalgenaf" ]; then # 2012/04, localpair --> local alignment distance
-#		if [ $distance = "global" ]; then
-#			distance="distonly"
-#		fi
-		if [ $treeout -eq 1 ]; then
-			parttreeoutopt="-t"
-			groupsize=1
-		else
-			parttreeoutopt=" "
-		fi
-		if [ $distout -eq 1 ]; then
-			distoutopt="-y -T"
-			if [ $treeout -eq 0 ]; then
-				treeoutopt=""
-			fi
-		fi
-	else
-		if [ $nodeout -eq 1 ]; then
-			if [ $iterate -gt 0 ]; then
-				echo "The --nodeout option supports only progressive method (--maxiterate 0) for now." 1>&2
-				exit 1
-			fi
-			parttreeoutopt="-t"
-			treeoutopt="-^"
-		elif [ $treeout -eq 1 ]; then
-			parttreeoutopt="-t"
-			treeoutopt="-t"
-		else
-			parttreeoutopt=" "
-			treeoutopt=" "
-		fi
-		if [ $distout -eq 1 ]; then
-			distoutopt="-y"
-		fi
-	fi
-#
-
-	formatcheck=`grep -c '^[[:blank:]]\+>' "$TMPFILE/infile" | head -1 `
-	if [ $formatcheck -gt 0 ]; then
-		echo "The first character of a description line must be " 1>&2
-		echo "the greater-than (>) symbol, not a blank."           1>&2
-		echo "Please check the format around the following line(s):"  1>&2
-		grep -n '^[[:blank:]]\+>' "$TMPFILE/infile"  1>&2
-		exit 1
-	fi
-
-	nseq=`grep -c '^[>|=]' "$TMPFILE/infile" | head -1 ` 
-	if [ $nseq -eq 2 ]; then
-		cycle=1
-	fi
-	if [ $cycle -gt 3 ]; then
-		cycle=3
-	fi
-
-	if [ $nseq -gt 60000 -a $iterate -gt 1 ]; then   # 2014/Oct/22, test
-		echo "Too many sequences to perform iterative refinement!" 1>&2
-		echo "Please use a progressive method." 1>&2
-		exit 1
-	fi
-	if [ $distance = "lastmulti" -o $distance = "multi" ]; then
-		if [ $fragment -eq 0 ]; then
-			echo 'Specify --addfragments too' 1>&2
-			exit 1
-		fi
-	fi
-
-	if [ $fragment -ne 0 ]; then
-		if [ $pairspecified -eq 0 ]; then
-			distance="multi"
-		fi
-		if [ $distance != "multi" -a $distance != "hybrid" -a $distance != "lastmulti" -a $distance != "local" -a $distance != "last" -a  $distance != "ktuples" -a $distance != "ktuplesmulti" ]; then
-			echo 'Specify --multipair, --lastmultipair, --lastpair, --localpair, --6merpair, --6mermultipair or --hybridpair' 1>&2
-			exit 1
-		fi
-	fi
-
-	if [ "$memopt" = " -M -B " -a "$distance" != "ktuples" ]; then
-		echo "Impossible" 1>&2
-		exit 1
-	fi
-
-	if [ $distance = "parttree" ]; then
-		if [ "$mergetable" != "/dev/null" ]; then
-			echo "The combination of (dp)parttree and merge is Impossible.  " 1>&2
-			exit 1
-		fi
-		if [ $addfile != "/dev/null" ]; then
-			echo "The combination of (dp)parttree and add(fragments) is Impossible.  " 1>&2
-			exit 1
-		fi
-		if [ $seed != "x" -o $seedtable != "x" ]; then
-			echo "Impossible" 1>&2
-			exit 1
-		fi
-		if [ $iterate -gt 1 ]; then
-			echo "Impossible" 1>&2
-			exit 1
-		fi
-		if [ $outorder = "aligned" ]; then
-			outorder="input"
-		fi
-		outorder="input"   # partorder ga kiku
-		if [ $partdist = "localalign" ]; then
-			splitopt=" -U "    # -U -l -> fast 
-			cycle=1
-		elif [ $partdist = "fasta" ]; then
-			splitopt=" -S "
-			cycle=1
-		else
-			splitopt="  "
-		fi
-	fi
-
-
-	if [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed = "x" -a $seedtable = "x" -a $ownlist = "/dev/null" -a $pdblist = "/dev/null" -a $enrichstr -eq 0 -a $newdash -eq 0 \) ]; then
-		localparam=""
-		weighti="0.0"
-	elif [ \( $distance = "ktuples" -o $distance = "ktuplesmulti" \) -a \( $seed != "x" -o $seedtable != "x" -o $ownlist != "/dev/null" -o $pdblist != "/dev/null" -o $enrichstr -eq 1 -o $newdash -eq 1 \) ]; then
-		if [ $cycle -lt 2 ]; then
-			cycle=2                # disttbfast ha seed hi-taiou #  chuui 2014Aug21
-		fi
-		if [ $iterate -lt 2 ]; then
-			echo "############################################################################" 1>&2
-			echo "# Warning:" 1>&2
-			echo "#   Progressive alignment method is incompatible with the --seed option." 1>&2
-			echo "#   Automatically switched to the iterative refinement method." 1>&2
-			echo "#   " 1>&2
-			echo "# Also consider using the '--add' option, which is compatible with" 1>&2
-			echo "#   the progressive method and FASTER than the '--seed' option." 1>&2
-			echo "#   Usage is:" 1>&2
-			echo "#   % mafft --add newSequences existingAlignment > output" 1>&2
-			echo "############################################################################" 1>&2
-			iterate=2
-		fi
-		localparam="-l "$weighti
-	elif [ $distance = "parttree" ]; then
-		localparam=""
-		weighti="0.0"
-		if [ $groupsize -gt -1 ]; then
-			cycle=1
-		fi
-	else
-#		localparam="-B -l "$weighti   # weighti=0 demo bunkatsu nashi
-		localparam="-l "$weighti   # -B (bunkatsunashi) ha dvtditr.c de taiou (17/Jan/15)
-		if [ $cycle -gt 1 ]; then  # 09/01/08
-			cycle=1
-		fi
-	fi
-
-
-	if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-		aof="0.000"
-		if [ $oldgenafparam -ne 1 ]; then
-			laof="0.0"
-			lexp="0.0"
-#			LEXP="0.0" # default = 0.0
-			usenaivepairscore="-Z"
-		fi
-	fi
-
-
-#	if [ $nseq -gt 5000 ]; then
-#		fft=0
-#	fi
-	if [ $forcefft -eq 1 ]; then
-		param_fft=" -G "
-		fft=1
-	elif [ $fft -eq 1 ]; then
-		param_fft=" -F "
-	else
-		param_fft=" "
-	fi
-
-	if [ $seed != "x" -a $seedtable != "x" ]; then
-			echo 'Use either one of seedtable and seed.  Not both.' 1>&2
-			exit 1
-	fi
-	if [ $f2clext = "-E" -a $anysymbol -gt 0 ]; then
-			echo '' 1>&2
-			echo 'The combination of --text and ( --anysymbol or --preservecase ) is impossible.' 1>&2
-			echo '' 1>&2
-			exit 1
-	fi
-
-#	if [ $f2clext = "-E" -a $scorematrix != "/dev/null" ]; then
-#			echo '' 1>&2
-#			echo 'At present, the combination of --text and (--aamatrix) is impossible.' 1>&2
-#			echo '' 1>&2
-#			exit 1
-#	fi
-
-	memsavetree=0
-	if [ $treeext != "none" ]; then
-		if [ $distance == "ktuples" ]; then
-			treein=1
-			treeinopt=" -U "
-			if [ $treeext == "randomchain" ]; then
-				echo "shuffle $randomseed" > "$TMPFILE/_guidetree"
-				cycle=1       #  disttbfast.c dem shitei
-			elif [ $treeext == "pileup" ]; then
-				echo "pileup" > "$TMPFILE/_guidetree"
-				cycle=1       #  disttbfast. shitei
-			elif [ $treeext == "memsavetree" ]; then
-				echo "very compact" > "$TMPFILE/_guidetree"
-				memsavetree=1
-			elif [ $treeext == "memsavetreex" ]; then
-				echo "compact " "$initialramusage" > "$TMPFILE/_guidetree"
-				memsavetree=1
-			elif [ $treeext == "stepadd" ]; then
-				echo "stepadd" > "$TMPFILE/_guidetree"
-				memsavetree=1
-			elif [ $treeext == "youngestlinkage" ]; then
-				echo "youngestlinkage" > "$TMPFILE/_guidetree"
-				memsavetree=1
-			else
-				echo "error in mafft.tmpl"
-				exit
-			fi
-		else # globalpair, localpair, genafpair, oldgenafpair
-#			treein, treeinopt ha kimaranai
-			if [ $treeext == "memsavetree" -o $treeext == "stepadd" ]; then
-				memsavetree=1
-			else
-				echo "With globalpair, localpair or genafpair," 1>>"$progressfile"
-				echo "Use --large, --minimumlinkage, --averagelinkage or --mixedlinkage." 1>>"$progressfile"
-				echo "--$treeext is supported only with --6merpair." 1>>"$progressfile"
-				echo '' 1>>"$progressfile"
-				exit
-			fi
-		fi
-		if [ $iterate -gt 0 ]; then
-			echo 'Iterative refinment is not supported for --large or --'$treeext  1>>"$progressfile"
-			echo '' 1>>"$progressfile"
-			exit 1
-		fi
-		if [ $fragment -ne 0 ]; then
-			echo '--addfragments, --addfull or --addlong is not yet supported for --large or --'$treeext  1>>"$progressfile"
-			echo "Use --add newsequences --$treeext" 1>>"$progressfile"
-			echo "Or, --addfragments (long, full) newsequences, without --"$treeext 1>>"$progressfile"
-			echo '' 1>>"$progressfile"
-			exit 1
-		fi
-		if [ "$mergetable" != "/dev/null" ]; then # 2018/Mar/2
-			echo '--merge is not yet supported for --large or --'$treeext  1>>"$progressfile"
-			echo "Use --merge without --"$treeext 1>>"$progressfile"
-			echo '' 1>>"$progressfile"
-			exit 1
-		fi
-	fi
-
-
-	if [ $nadd -gt "0" ]; then
-		if [ $fragment -eq "1" ]; then
-			addarg="$addarg0 $nadd -g -0.01"
-			addsinglearg=""
-			cycle=1 # chuui 2014Aug25
-			iterate=0
-		elif [ $fragment -eq "-1" ]; then
-			addarg="$addarg0 $nadd"
-			addsinglearg="-V"       # allowlongadds, 2014/04/02
-			cycle=1 # chuui 2014Aug25
-			iterate=0
-		elif [ $fragment -eq "-2" ]; then
-			addarg="$addarg0 $nadd"
-			addsinglearg="-V"       # allowlongadds + smoothing
-			add2ndhalfarg=$add2ndhalfarg" -p "
-			cycle=1 # chuui 2014Aug25
-			usenaivepairscore="-Z" # 2015Jun01
-			laof=0.0               # 2015Jun01
-			lexp=0.0               # 2015Jun01
-			iterate=0
-		else
-			addarg="$addarg0 $nadd"
-			addsinglearg=""
-#			iterate=1 # iterate ha shitei dori
-			bunkatsuopt=" -B "  # fftnsi demo bunktasu shinai
-			if [ "$add2ndhalfarg" != " " ]; then
-				if [ $auto -eq 1 -o $iterate -gt 0 ]; then
-					echo '' 1>>"$progressfile"
-					echo 'The --keeplength and --mapout options are not supported' 1>>"$progressfile"
-					echo 'with the --auto or --maxiterate >0 options.' 1>>"$progressfile"
-					echo 'Use the --maxiterate 0 option (= progressive method).' 1>>"$progressfile"
-					echo '' 1>>"$progressfile"
-					exit 1
-				fi
-			fi
-		fi
-		
-
-#		cycle=1 # chuui 2014Aug19
-#		iterate=0
-#		treealg=" -q "  ## 2012/01/24  ## removed 2012/02/06
-	else
-		if [ "$add2ndhalfarg" != " " ]; then
-			echo '' 1>>"$progressfile"
-			echo 'The --keeplength and --mapout options are supported' 1>>"$progressfile"
-			echo 'only with --add, --addfragments or --addlong.' 1>>"$progressfile"
-			echo '' 1>>"$progressfile"
-			exit 1
-		fi
-	fi
-
-
-	if [ -z "$localparam" -a $fragment -eq 0 -a $distance != "parttree" ]; then
-#		echo "use disttbfast"
-#		echo cycle = $cycle
-		cycletbfast=1            # tbfast wo jikkou shinai
-		cycledisttbfast=$cycle   # disttbfast ni -E cycle wo watasu
-		if [ $cycledisttbfast -eq 0 ]; then # --treeout de tsukau
-			cycledisttbfast=1
-		fi
-	else
-#		echo "use tbfast"
-#		echo cycle = $cycle
-		cycletbfast=$cycle       # 1 ijou nara jikkou
-		cycledisttbfast=1        # disttbfast ha ikkai dake
-	fi
-
-#	echo localparam=
-#	echo $localparam
-#	echo cycletbfast=
-#	echo $cycletbfast
-#	echo cycledisttbfast=
-#	echo $cycledisttbfast
-
-#exit
-
-	if [ $adjustdirection -gt 0 -a $seed != "x" ]; then
-			echo '' 1>&2
-			echo 'The combination of --adjustdirection(accurately) and --seed is not supported.' 1>&2
-			echo '' 1>&2
-			exit 1
-	fi
-
-
-	if [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
-		if [ $distance = "ktuples" ]; then
-			echo 'Not supported.' 1>&2
-			echo 'Please add --globalpair, --localpair, --scarnapair, --dafspair' 1>&2
-			echo '--larapair, --slarapair, --foldalignlocalpair or --foldalignglobalpair' 1>&2
-			exit 1
-		fi
-		if [ $f2clext = "-E" ]; then
-				echo '' 1>&2
-				echo 'For RNA alignment, the --text mode is impossible.' 1>&2
-				echo '' 1>&2
-				exit 1
-		fi
-	fi
-
-# cycle ga atode henkou sareru node koko de strategy no namae wo kimeru.
-# kokokara
-	if [ $treeext = "pileup" ]; then
-		strategy="Pileup-"
-	elif [ $treeext = "randomchain" ]; then
-		strategy="Randomchain-"
-	elif [ $mccaskill -eq 1 -o $dafs -eq 1 -o $rnaalifold -eq 1 -o $contrafold -eq 1 ]; then
-		if [ $distance = "scarna" -o $distance = "dafs" -o $distance = "lara" -o $distance = "slara" -o $distance = "foldalignlocal" -o $distance = "foldalignglobal" ]; then
-			strategy="X-"
-		elif [ $distance = "global" -o $distance = "local" -o $distance = "localgenaf" -o "globalgenaf" ]; then
-			strategy="Q-"
-		fi
-	elif [ $distance = "fasta" -a $sw -eq 0 ]; then
-		strategy="F-"
-	elif [ $distance = "fasta" -a $sw -eq 1 ]; then
-		strategy="H-"
-	elif [ $distance = "blast" ]; then
-		strategy="B-"
-	elif [ $distance = "global" -o $distance = "distonly" ]; then
-		strategy="G-"
-	elif [ $distance = "local" ]; then
-		strategy="L-"
-	elif [ $distance = "last" ]; then
-		strategy="Last-"
-	elif [ $distance = "hybrid" ]; then
-		strategy="Hybrid-"
-	elif [ $distance = "multi" ]; then
-		strategy="Multi-"
-	elif [ $distance = "lastmulti" ]; then
-		strategy="LastMulti-"
-	elif [ $distance = "localgenaf" ]; then
-		strategy="E-"
-	elif [ $distance = "globalgenaf" ]; then
-		strategy="K-"
-	elif [ $fft -eq 1 ]; then
-		strategy="FFT-"
-	else
-		strategy="NW-"
-	fi
-	if [ $memsavetree -eq 1 ]; then
-		strategy=$strategy"large-"
-	fi
-#	if [ `echo "$weighti>0.0" | bc` -gt 0 ]; then
-	if [ `awk "BEGIN {print(0.0+\"$weighti\">0.0)}"` -gt 0 ]; then
-		strategy=$strategy"I"
-	fi
-	strategy=$strategy"NS-"
-	if [ $iterate -gt 0 ]; then
-		strategy=$strategy"i"
-	elif [ $distance = "parttree" ]; then
-		if [ $partdist = "fasta" ]; then
-			strategy=$strategy"FastaPartTree-"$cycle
-		elif [ $partdist = "localalign" ]; then
-			strategy=$strategy"DPPartTree-"$cycle
-		else
-			strategy=$strategy"PartTree-"$cycle
-		fi
-	elif [ $fragment -eq 1 ]; then
-		strategy=$strategy"fragment"
-	elif [ $fragment -eq -1 ]; then
-		strategy=$strategy"full"
-	elif [ $fragment -eq -2 ]; then
-		strategy=$strategy"long"
-	else
-		strategy=$strategy$cycle
-	fi
-
-	explanation='?'
-	performance='Not tested.'
-	if [ $strategy = "F-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
-		performance='Most accurate, but very slow'
-	elif [ $strategy = "L-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment information'
-		performance='Probably most accurate, very slow'
-	elif [ $strategy = "E-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with LOCAL pairwise alignment with generalized affine gap costs (Altschul 1998)'
-		performance='Suitable for sequences with long unalignable regions, very slow'
-	elif [ $strategy = "G-INS-i" ]; then
-		explanation='Iterative refinement method (<'$iterate') with GLOBAL pairwise alignment information'
-		performance='Suitable for sequences of similar lengths, very slow'
-	elif [ $strategy = "X-INS-i" ]; then
-		explanation='RNA secondary structure information is taken into account.'
-		performance='For short RNA sequences only, extremely slow'
-	elif [ $strategy = "F-INS-1" ]; then
-		explanation='Progressive method incorporating LOCAL pairwise alignment information'
-	elif [ $strategy = "L-INS-1" ]; then
-		explanation='Progressive method incorporating LOCAL pairwise alignment information'
-	elif [ $strategy = "G-INS-1" ]; then
-		explanation='Progressive method incorporating GLOBAL pairwise alignment information'
-	elif [ $strategy = "FFT-NS-i" -o $strategy = "NW-NS-i" ]; then
-		explanation='Iterative refinement method (max. '$iterate' iterations)'
-		if [ $iterate -gt 2 ]; then
-			performance='Accurate but slow'
-		else
-			performance='Standard'
-		fi
-	elif [ $strategy = "FFT-NS-2" -o $strategy = "NW-NS-2" ]; then
-		explanation='Progressive method (guide trees were built '$cycle' times.)'
-		performance='Fast but rough'
-	elif [ $strategy = "FFT-NS-1" -o $strategy = "NW-NS-1" ]; then
-		explanation='Progressive method (rough guide tree was used.)'
-		performance='Very fast but very rough'
-	fi
-
-	if [ $outputformat = "clustal" -a $outorder = "aligned" ]; then
-		outputopt=" -c $strategy -r $TMPFILE/order $f2clext "
-	elif [ $outputformat = "clustal" -a $outorder = "input" ]; then
-		outputopt=" -c $strategy  $f2clext "
-	elif [ $outputformat = "phylip" -a $outorder = "aligned" ]; then
-		outputopt=" -y -r $TMPFILE/order "
-	elif [ $outputformat = "phylip" -a $outorder = "input" ]; then
-		outputopt=" -y "
-	elif [ $outputformat = "pir" -a $outorder = "aligned" ]; then
-		outputopt=" -f -r $TMPFILE/order "
-	else
-		outputopt="-f"
-	fi
-
-	if [ $newdash_originalsequenceonly -eq 1 ]; then
-		outputopt="$outputopt  -d "
-	fi
-# kokomade
-
-	
-	
-		pushd "$TMPFILE" > /dev/null
-
-		cat /dev/null > pre
-
-#		echo "nseq = " $nseq              1>>"$progressfile"
-#		echo "distance = " $distance      1>>"$progressfile"
-#		echo "iterate = " $iterate        1>>"$progressfile"
-#		echo "cycle = " $cycle            1>>"$progressfile"
-
-		if [ $anysymbol -eq 1 ]; then
-			mv infile orig
-			"$prefix/replaceu" $seqtype -i orig > infile 2>>"$progressfile" || exit 1
-		fi
-
-		if [ $mergetable != "/dev/null" ]; then
-			if [ $nadd -gt "0" ]; then
-				echo "Impossible" 1>&2
-				exit 1
-			fi
-#			if [ $seed != "x" -o $seedtable != "x" ]; then
-#				echo "This version does not support the combination of merge and seed." 1>&2
-#				exit 1
-#			fi
-#			iterate=0 # 2013/04/16
-			mergearg="-H $seedoffset"
-		fi
-
-		if [ $adjustdirection -gt 0 ]; then
-			if [ $fragment -ne 0 ]; then
-				fragarg="-F" #
-			else
-				fragarg="-F" # 2014/02/06, do not consider other additional sequences, even in the case of --add
-			fi
-			if [ $adjustdirection -eq 1 ]; then
-				"$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 5000 -o a > _direction 2>>"$progressfile"
-			elif [ $adjustdirection -eq 2 ]; then
-				"$prefix/makedirectionlist" $fragarg -C $numthreads -m -I $nadd -i infile -t 0.00 -r 100 -o a -d > _direction 2>>"$progressfile"
-			fi
-			"$prefix/setdirection" $mergearg -d _direction -i infile > infiled 2>>"$progressfile" || exit
-			mv infiled infile
-			if [ $anysymbol -eq 1 ]; then
-				"$prefix/setdirection" $mergearg -d _direction -i orig -r  > origd 2>>"$progressfile" || exit
-				mv origd orig
-			fi
-		fi
-
-		if [ $seed != "x" -o $seedtable != "x" ]; then
-			if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
-				echo "The combination of --seed and (--pdbidlist or --pdbfilelist) is impossible."  1>>"$progressfile"
-				exit 1
-			fi
-#			if [ $enrich -eq 1 ]; then
-#				echo "The combination of --seed and (--enrich, --enrichseq or --enrichstr) is impossible at present."  1>>"$progressfile"
-#				exit 1
-#			fi
-
-			if [ $newdash -eq 1 ]; then
-				echo "The combination of --seed and --dash is impossible at present."  1>>"$progressfile"
-				exit 1
-			fi
-		fi
-
-
-#		if [ $enrich -eq 1 ]; then
-#			if [ $ownlist != "/dev/null" ]; then
-#				echo "Warning: Sequence homologs of the structures given with the --pdbfilelist option cannot be collected.\n" 1>>"$progressfile"
-#			fi
-#			echo "SEEKQUENCER (http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/) is" 1>>"$progressfile"
-#			if [ $pdblist != "/dev/null" ]; then
-#				echo "collecting homoplogs of the input sequences and the structures given with the --pdbidlist option." 1>>"$progressfile"
-#				perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -idf pdblist -out seekout -mod mafftash-split 2>>"seekerr"
-#				seekres="$?"
-#			else
-#				echo "collecting homologs of the input sequences." 1>>"$progressfile"
-#				perl "$prefix/seekquencer_premafft.pl" $seektarget -run thread -trd 2 -seqd uniref90 -blim 1000 -noin -seqf infile -out seekout -mod mafftash-split 2>>"seekerr"
-#				seekres="$?"
-#			fi
-#			cat seekerr  1>>"$progressfile"
-#
-#			if [ $seekres -ne "0" ]; then
-#				echo "Error in SEEKQUENCER" 1>>"$progressfile"
-#				exit 1;
-#			fi
-#			echo "Done." 1>>"$progressfile"
-#
-#			if [ $enrichseq -eq 1 ]; then
-##				cat seekout.seq >> infile
-#				if [ $anysymbol -eq 1 ]; then
-#					"$prefix/replaceu" $seqtype -i seekout.seq -o $nseq >> infile
-#					cat seekout.seq >> orig
-#				else
-#					"$prefix/replaceu" $seqtype -i seekout.seq | sed 's/_os_[0-9]*_oe_//' >> infile
-#				fi
-#
-#			fi
-#			if [ $enrichstr -eq 1 ]; then
-#				nseekstr=`wc -l < seekout.str`
-#				if [ $nseekstr -gt 1 ]; then
-#					cat seekout.str >> pdblist
-#					pdblist="tsukaimasu"
-#				fi
-#			fi
-#		fi
-
-		if [ $seed != "x" ]; then
-			mv infile infile2
-			if [ $anysymbol -eq 1 ]; then
-				mv orig orig2
-				cat /dev/null > orig
-			fi
-			cat /dev/null > infile
-			cat /dev/null > hat3.seed
-			seedoffset=0
-#			echo "seednseq="$seednseq
-#			echo "seedoffset="$seedoffset
-			set $seednseq >> "$progressfile"
-#			echo $#
-			while [ $# -gt 1 ]
-			do
-				shift
-#				echo "num="$#
-
-				if [ $anysymbol -eq 1 ]; then
-					cat seed$# >> orig
-					"$prefix/replaceu" $seqtype -i seed$# -o $seedoffset > clean 2>>"$progressfile" || exit 1
-					mv clean seed$#
-				fi
-				"$prefix/multi2hat3s" -t $nseq -o $seedoffset -i seed$# >> infile 2>>"$progressfile" || exit 1
-				cat hat3 >> hat3.seed
-#				echo "$1"
-				seedoffset=`expr $seedoffset + $1`
-#				echo "$1"
-#				echo "seedoffset="$seedoffset
-			done;
-#			echo "seedoffset="$seedoffset
-			if [ $anysymbol -eq 1 ]; then
-				"$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1  # yarinaoshi
-				cat orig2 >> orig
-			else
-				cat infile2 >> infile
-			fi
-		elif [ $seedtable != "x" ]; then
-			cat _seedtablefile > hat3.seed
-		elif [ $newdash -eq 1 ]; then
-			seemstobe=`"$prefix/countlen" -i infile | awk '{print $6}'`
-			if [ $seemstobe = "d" -a "x$seqtype" != "x-P" ]; then
-				echo "" 1>>"$progressfile"
-				echo "Error: This data seems to be nucleotide sequences." 1>>"$progressfile"
-				echo "Add the --amino flag if this is surely protein." 1>>"$progressfile"
-				echo "" 1>>"$progressfile"
-				exit 1;
-			fi
-			if [ $anysymbol -eq 1 ]; then
-				mv orig infile # replaceu wo mukouka
-			fi
-			sed 's/-//g' infile > dashin # gap nozoku
-
-			if [ ! -x "$prefix/dash_client" -o ! -x "$prefix/dash_client" ]; then
-				echo ""       1>&2
-				echo "== Install DASH client =====================================================" 1>&2
-				echo "To use this feature, uncomment the following line in Makefile"                1>&2
-				echo "DASH_CLIENT = dash_client"                                                    1>&2
-				echo "and re-compile the source."                                                   1>&2
-				echo "Note that it requires the 'Go' compiler."                                     1>&2
-				echo "============================================================================" 1>&2
-				echo "" 1>&2
-				exit 1
-			fi
-			
-			echo "Calling DASH (https://sysimm.org/dash/)" 1>>"$progressfile"
-			"$prefix/dash_client" -i dashin -sequences dashsequences -hat3 hat3.seed 1>>"$progressfile"
-			dashres="$?"
-			if [ $dashres -ne "0" ]; then
-				echo "Error in DASH" 1>>"$progressfile"
-				echo "To use this feature, compiled with" 1>>"$progressfile"
-				exit 1;
-			fi
-
-			if [ $exclude_ho -eq 1 ]; then # amari yokunai
-				awk 'BEGIN{out=1} !/^>_addedbymaffte_/{if(out) print; out=1} /^>_addedbymaffte_/{out=0}' dashsequences | sed 's/>DASH_/>DASH|/' > ho_excluded
-				mv ho_excluded dashsequences
-			fi
-
-			if [ "$mergetable" != "/dev/null" ]; then # 2020/Apr/30
-				ndash=`grep -c '>DASH_' dashsequences | head -1`
-#				echo "ndash = " $ndash
-				awk "{for( i=1;i<=NF;i++){if(0+\$i==0)break; printf( \"%d \", $ndash+\$i); } print \"\" }" _subalignmentstable > _subalignmentstableshifted
-				mv _subalignmentstableshifted _subalignmentstable
-				cp dashsequences dashsequences.bk
-				awk "BEGIN{nout=0} {if(\$1~/^>/) nout++; if( nout <= $ndash ) print;}" dashsequences > infile2
-				cat infile >> infile2
-				cp infile2 dashsequences
-			fi
-
-			sed 's/>DASH_/>DASH|/' dashsequences > renamed
-			mv renamed dashsequences
-			echo "Done." 1>>"$progressfile"
-#			cat  hat3.seed
-			seedoffset=`grep -c '^[>|=]' dashsequences | head -1 ` 
-			echo "# of structures = " 1>>"$progressfile"
-			echo $seedoffset 1>>"$progressfile"
-			if [ $anysymbol -eq 1 ]; then
-				cat dashsequences >> orig
-				"$prefix/replaceu" $seqtype -i dashsequences -o 0 > clean 2>>"$progressfile" || exit 1
-				mv clean infile
-
-#				"$prefix/replaceu" $seqtype -i orig2 -o $seedoffset >> infile 2>>"$progressfile" || exit 1  # yarinaoshi
-#				cat orig2 >> orig
-			else
-				cat dashsequences > infile
-#				cat infile2 >> infile
-			fi
-		else
-			cat /dev/null > hat3.seed
-		fi
-#		cat hat3.seed
-
-		if [ $mccaskill -eq 1 ]; then
-			"$prefix/mccaskillwrap" -s -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
-		elif [ $dafs -eq 1 ]; then
-			"$prefix/mccaskillwrap" -G -C $numthreads -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
-		elif [ $contrafold -eq 1 ]; then
-			"$prefix/contrafoldwrap" -d "$prefix" -i infile > hat4 2>>"$progressfile" || exit 1
-		fi
-		if [ $distance = "fasta" ]; then
-			"$prefix/dndfast7" $swopt < infile > /dev/null  2>>"$progressfile"    || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "blast" ]; then
-			"$prefix/dndblast" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "foldalignlocal" ]; then
-			"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $lexp -f $lgop -Q $spfactor -h $laof -H -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "foldalignglobal" ]; then
-			"$prefix/pairlocalalign" -C $numthreads $seqtype $foldalignopt $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof -H -o -global -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "slara" ]; then
-			"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop -Q $spfactor -T -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "lara" ]; then
-			"$prefix/pairlocalalign" -C $numthreads -p $laraparams  $seqtype $model  -f $lgop -Q $spfactor -B -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "scarna" ]; then
-#			"$prefix/pairlocalalign"   -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -s -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-#			cat hat3.seed hat3 > hatx
-#			mv hatx hat3
-#			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			"$prefix/tbfast" _  -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -s -d "$prefix" _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "dafs" ]; then
-			"$prefix/pairlocalalign"  -C $numthreads $seqtype $model  -f $pggop -Q $spfactor -G -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "global" -a $memsavetree -eq 1 ]; then
-			if [ "$mpiscript" !=  "/dev/null" ]; then
-				sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg $treeinopt $treeoutopt  -i  infile > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/nodepair"  $lhlimit -u $unalignlevel $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg $treeinopt $treeoutopt  -i  infile   > /dev/null 2>>"$progressfile" || exit 1
-			fi
-			echo 'nodepair' > _guidetree
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "local" -a $memsavetree -eq 1 ]; then
-			if [ "$mpiscript" !=  "/dev/null" ]; then
-				sh $mpiscript "$prefix/nodepair_mpi" $lhlimit -u $unalignlevel $localparam $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile   > /dev/null 2>>"$progressfile" || exit 1
-			fi
-
-			echo 'nodepair' > _guidetree
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "localgenaf" -a $memsavetree -eq 1 ]; then
-			"$prefix/nodepair" $lhlimit -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg $treeinopt $treeoutopt -i infile > /dev/null  2>>"$progressfile"      || exit 1
-			echo 'nodepair' > _guidetree
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt -U $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "global" -a $memsavetree -eq 0 ]; then
-			"$prefix/tbfast" _  -u $unalignlevel $localparam  -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -A  $usenaivepairscore $focusarg  _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			
-		elif [ $distance = "local" -a $memsavetree -eq 0 ]; then
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/pairlocalalign" $localparam $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore < infile > /dev/null  2>>"$progressfile"      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/tbfast" _  -u $unalignlevel $localparam -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -L $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			fi
-		elif [ $distance = "globalgenaf" ]; then
-			"$prefix/pairlocalalign"  -u $unalignlevel $localparam -C $numthreads $seqtype $model  -g $pgexp -f $pggop -Q $spfactor -h $pgaof -O $GGOP -E $GEXP -K $usenaivepairscore < infile > /dev/null 2>>"$progressfile"    || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "localgenaf" -a $memsavetree -eq 0 ]; then
-			"$prefix/tbfast" _ -u $unalignlevel $localparam -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof -O $LGOP -E $LEXP -N $usenaivepairscore $focusarg _ -+ $iterate -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg $focusarg < infile > /dev/null  2>>"$progressfile"      || exit 1
-		elif [ $distance = "last" ]; then
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/pairlocalalign" -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -R $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-#				addarg wo watasanai
-				cat hat3.seed hat3 > hatx
-				mv hatx hat3
-				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			fi
-		elif [ $distance = "lastmulti" ]; then
-			"$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -Q $spfactor -h $laof < infile > /dev/null 2>>"$progressfile"      || exit 1
-			mv hat2 hat2i
-			"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model -e $last_e -w $last_m -g $lexp -f $lgop -Q $spfactor -h $laof -r $last_subopt $last_once -d "$prefix" < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hat2 hat2n
-			mv hatx hat3
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				echo "Impossible" 1>&2
-				exit 1
-			fi
-		elif [ $distance = "multi" ]; then
-			"$prefix/dndpre" $model -M 2 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof  $usenaivepairscore < infile > /dev/null 2>>"$progressfile"      || exit 1
-			mv hat2 hat2i
-			"$prefix/pairlocalalign" $localparam $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -Y $usenaivepairscore < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hat2 hat2n
-			mv hatx hat3
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				echo "Impossible" 1>&2
-				exit 1
-			fi
-		elif [ $distance = "hybrid" ]; then
-			"$prefix/pairlocalalign" $addarg   -C $numthreads $seqtype $model  -g $lexp -f $lgop -Q $spfactor -h $laof -Y < infile > /dev/null  2>>"$progressfile"      || exit 1
-			cat hat3.seed hat3 > hatx
-			mv hatx hat3
-			"$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/addsingle" -Q 100 $legacygapopt -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			fi
-#		elif [ $distance = "distonly" ]; then
-#			"$prefix/pairlocalalign"   -C $numthreads $seqtype $model -g $pgexp -f $pggop -Q $spfactor -h $pgaof  -t < infile > /dev/null  2>>"$progressfile"      || exit 1
-#			"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $outnum $addarg $add2ndhalfarg -C $numthreadstb $rnaopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-		elif [ $distance = "parttree" ]; then
-			"$prefix/splittbfast" $legacygapopt $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof -p $partsize -s $groupsize $treealg $outnum -i infile   > pre 2>>"$progressfile" || exit 1
-			mv hat3.seed hat3
-		elif [ $distance = "ktuplesmulti" ]; then
-#			"$prefix/dndpre" $model -M 1 $addarg -C $numthreads $seqtype $model -g $lexp -f $lgop -h $laof < infile > /dev/null 2>>"$progressfile"      || exit 1
-#			mv hat2 hat2i
-#			"$prefix/disttbfast" -E 1 -s $unalignlevel $legacygapopt -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt -T -y $seqtype $model -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-#			mv hat2 hat2n
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/addsingle" -Q 100 $legacygapopt -d -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-#				"$prefix/addsingle" -Q 100 $legacygapopt -d -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				echo "Impossible" 1>&2
-				exit 1
-			fi
-		else
-			if [ $fragment -ne 0 ]; then 
-				"$prefix/addsingle" -Q 100 $legacygapopt -W $tuplesize -O $outnum $addsinglearg $addarg $add2ndhalfarg -C $numthreads $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -f "-"$gop  -h $aof  $param_fft $localparam   $algopt $treealg $scoreoutarg < infile   > /dev/null 2>>"$progressfile" || exit 1
-			else
-				"$prefix/disttbfast" -q $npickup -E $cycledisttbfast -V "-"$gopdist  -s $unalignlevel $legacygapopt $mergearg -W $tuplesize $termgapopt $outnum $addarg $add2ndhalfarg -C $numthreads-$numthreadstb $memopt $weightopt $treeinopt $treeoutopt $distoutopt $seqtype $model -g $gexp -f "-"$gop -Q $spfactor -h $aof  $param_fft $algopt $treealg $scoreoutarg $anchoropt -x $maxanchorseparation $oneiterationopt < infile   > pre 2>>"$progressfile" || exit 1
-				mv hat3.seed hat3
-			fi
-		fi
-		while [ $cycletbfast -gt 1 ]
-		do
-			if [ $distance = "parttree" ]; then
-				mv pre infile
-				"$prefix/splittbfast" $legacygapopt -Z $algopt $splitopt $partorderopt $parttreeoutopt $memopt $seqtype $model -f "-"$gop -Q $spfactor -h $aof  -p $partsize -s $groupsize $treealg $outnum -i infile   > pre 2>>"$progressfile" || exit 1
-			else
-				"$prefix/tbfast" -W $minimumweight -V "-"$gopdist -s $unalignlevel $legacygapopt $mergearg $termgapopt $outnum -C $numthreadstb $rnaopt $weightopt $treeoutopt $distoutopt $memopt $seqtype $model  -f "-"$gop -Q $spfactor -h $aof $param_fft  $localparam $algopt -J $treealg $scoreoutarg < pre > /dev/null 2>>"$progressfile" || exit 1
-# fragment>0 no baai, nanimoshinai
-# seed youchuui!!
-			fi
-			cycletbfast=`expr $cycletbfast - 1`
-		done
-		if [ $iterate -gt 0 ]; then
-			if [ $distance = "ktuples" ]; then
-			    "$prefix/dndpre" $seqtype $model -M 2 -C $numthreads < pre     > /dev/null 2>>"$progressfile" || exit 1
-			fi
-			"$prefix/dvtditr" -W $minimumweight $bunkatsuopt -E $fixthreshold -s $unalignlevel  $legacygapopt $mergearg $outnum -C $numthreadsit -t $randomseed $rnaoptit $memopt $scorecalcopt $localparam -z 50 $seqtype $model -f "-"$gop -Q $spfactor -h $aof  -I $iterate $weightopt $treeinopt $algoptit $treealg -p $parallelizationstrategy  $scoreoutarg  -K $nadd < pre     > /dev/null 2>>"$progressfile" || exit 1
-		fi
-		if [ $coreout -eq 1 ]; then
-			"$prefix/setcore" -w $corewin -i $corethr $coreext < pre > pre2
-			mv pre2 pre
-		elif [ $anysymbol -eq 1 ]; then
-			"$prefix/restoreu" $add2ndhalfarg -a pre -i orig > restored || exit 1
-			mv restored pre
-		fi
-
-
-
-
-		echo '' 1>>"$progressfile"
-		if [ $mccaskill -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the McCaskill algorithm (1)" 1>>"$progressfile"
-			echo "implemented in Vienna RNA package (2) and MXSCARNA (3), and then" 1>>"$progressfile"
-			echo "incorporated in the iterative alignment process (4)." 1>>"$progressfile"
-			echo "(1) McCaskill, 1990, Biopolymers 29:1105-1119" 1>>"$progressfile"
-			echo "(2) Hofacker et al., 2002, J. Mol. Biol. 319:3724-3732" 1>>"$progressfile"
-			echo "(3) Tabei et al., 2008, BMC Bioinformatics 9:33" 1>>"$progressfile"
-			echo "(4) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
-			echo "" 1>>"$progressfile"
-		elif [ $contrafold -eq 1 ]; then
-			echo "RNA base pairing probaility was calculated by the CONTRAfold algorithm (1)" 1>>"$progressfile"
-			echo "and then incorporated in the iterative alignment process (4)." 1>>"$progressfile"
-			echo "(1) Do et al., 2006, Bioinformatics 22:e90-98" 1>>"$progressfile"
-			echo "(2) Katoh and Toh, 2008, BMC Bioinformatics 9:212" 1>>"$progressfile"
-			echo "" 1>>"$progressfile"
-		fi
-		if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
-			echo "Input structures are decomposed into structural domains using" 1>>"$progressfile"
-			echo "Protein Domain Parser (Alexandrov & Shindyalov 2003)."         1>>"$progressfile"
-			echo "Domain pairs are aligned using the rash function in"           1>>"$progressfile"
-			echo "the ASH structural alignment package (Standley et al. 2007)."  1>>"$progressfile"
-		fi
-		if [ $pdblist != "/dev/null" ]; then
-			echo "Pre-computed alignments stored in "                            1>>"$progressfile"
-			echo "DASH (http://sysimm.ifrec.osaka-u.ac.jp/dash/) are used. "     1>>"$progressfile"
-		fi
-		if [ $distance = "fasta" -o $partdist = "fasta" ]; then
-			echo "Pairwise alignments were computed by FASTA" 1>>"$progressfile"
-			echo "(Pearson & Lipman, 1988, PNAS 85:2444-2448)" 1>>"$progressfile"
-		fi
-		if [ $distance = "blast" ]; then
-			echo "Pairwise alignments were computed by BLAST" 1>>"$progressfile"
-			echo "(Altschul et al., 1997, NAR 25:3389-3402)" 1>>"$progressfile"
-		fi
-		if [ $distance = "last" -o $distance = "lastmulti" ]; then
-			echo "Pairwise alignments were computed by LAST" 1>>"$progressfile"
-			echo "http://last.cbrc.jp/" 1>>"$progressfile"
-			echo "Kielbasa, Wan, Sato, Horton, Frith 2011 Genome Res. 21:487" 1>>"$progressfile"
-		fi
-		if [ $distance = "scarna" ]; then
-			echo "Pairwise alignments were computed by MXSCARNA" 1>>"$progressfile"
-			echo "(Tabei et al., 2008, BMC Bioinformatics 9:33)." 1>>"$progressfile"
-		fi
-		if [ $distance = "dafs" ]; then
-			echo "Pairwise alignments were computed by DAFS" 1>>"$progressfile"
-			echo "(Sato et al., 2012,,,,)." 1>>"$progressfile"
-		fi
-		if [ $distance = "lara" -o $distance = "slara" ]; then
-			echo "Pairwise alignments were computed by LaRA" 1>>"$progressfile"
-			echo "(Bauer et al., 2007, BMC Bioinformatics 8:271)." 1>>"$progressfile"
-		fi
-		if [ $distance = "foldalignlocal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (local)" 1>>"$progressfile"
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
-		fi
-		if [ $distance = "foldalignglobal" ]; then
-			echo "Pairwise alignments were computed by FOLDALIGN (global)" 1>>"$progressfile"
-			echo "(Havgaard et al., 2007, PLoS Computational Biology 3:e193)." 1>>"$progressfile"
-		fi
-#		printf "\n" 1>>"$progressfile"
-		echo 'Strategy:' 1>>"$progressfile"
-		printf ' '$strategy 1>>"$progressfile"
-		echo ' ('$performance')' 1>>"$progressfile"
-		echo ' '$explanation 1>>"$progressfile"
-		echo '' 1>>"$progressfile"
-		echo "If unsure which option to use, try 'mafft --auto input > output'." 1>>"$progressfile"
-		echo "For more information, see 'mafft --help', 'mafft --man' and the mafft page." 1>>"$progressfile"
-		echo "" 1>>"$progressfile"
-		echo "The default gap scoring scheme has been changed in version 7.110 (2013 Oct)." 1>>"$progressfile"
-		echo "It tends to insert more gaps into gap-rich regions than previous versions." 1>>"$progressfile"
-		echo "To disable this change, add the --leavegappyregion option." 1>>"$progressfile"
-#		echo "If long gaps are expected, try 'mafft --ep 0.0 --auto input > output'." 1>>"$progressfile"
-#		echo "If the possibility of long gaps can be excluded, add '--ep 0.123'." 1>>"$progressfile"
-		if [ $distance = "localgenaf" -o $distance = "globalgenaf" ]; then
-			echo "" 1>>"$progressfile"
-			if [ $oldgenafparam -eq 1 ]; then
-				echo "Obsolete parameters used for this calculation." 1>>"$progressfile"
-				echo "Also try the new parameters for E-INS-i, by not specifying --oldgenafpair." 1>>"$progressfile"
-			else
-				echo "Parameters for the E-INS-i option have been changed in version 7.243 (2015 Jun)." 1>>"$progressfile"
-				echo "To switch to the old parameters, use --oldgenafpair, instead of --genafpair." 1>>"$progressfile"
-			fi
-		fi
-		echo '' 1>>"$progressfile"
-
-		
-		if [ $pdblist != "/dev/null" -o $ownlist != "/dev/null" ]; then
-#			cat dasherr >>"$progressfile"
-			echo '' >>"$progressfile"
-		fi
-
-	popd > /dev/null
-
-	if [ "$outputopt" != "-f" -o "$windows" = "yes" ]; then # Windows deha kaigyo code wo f2cl de modosu.
-#		ln -s "$TMPFILE/order" _order$$ # f2cl ga space ari filename ni taiou shiteinainode
-#		cp "$TMPFILE/order" _order$$ # ln -s no error wo sakeru
-		if [ "$outputfile" = "" ]; then
-			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" 2>"/dev/null" || exit 1
-		else
-			"$prefix/f2cl" -n $namelength $outputopt < "$TMPFILE/pre" > "$outputfile" 2>"/dev/null" || exit 1
-		fi
-#		rm _order$$
-	else
-		if [ "$outputfile" = "" ]; then
-			cat < "$TMPFILE/pre" || exit 1
-		else
-			cat < "$TMPFILE/pre" > "$outputfile" || exit 1
-		fi
-	fi
-
-	if [ $treeout -eq 1 ]; then
-		cp "$TMPFILE/infile.tree" "$infilename.tree"
-	fi
-
-	if [ -s "$TMPFILE/GuideTree" ]; then # --merge no toki dake
-		cp "$TMPFILE/GuideTree" .
-	fi
-
-	if [ $distout -eq 1 ]; then
-		cp "$TMPFILE/hat2" "$infilename.hat2"
-	fi
-
-	if [ $npickup -ne 0 ]; then
-		cp "$TMPFILE/notused" "$infilename.notused"
-	fi
-
-	if [ -s "$TMPFILE/_deletemap" ]; then
-		if [ "$mapoutfile" = "/dev/null" ]; then
-			cp "$TMPFILE/_deletemap" "$addfile.map"
-		else
-			cp "$TMPFILE/_deletemap" "$mapoutfile"
-		fi
-	fi
-
-	exit 0;
-fi
-
-prog="awk"
-
-#tmpawk=`which nawk 2>/dev/null | awk '{print $1}'`
-#if [ -x "$tmpawk" ]; then
-#	prog="$tmpawk"
-#fi
-#
-#tmpawk=`which gawk 2>/dev/null | awk '{print $1}'`
-#if [ -x "$tmpawk" ]; then
-#	prog="$tmpawk"
-#fi
-# 2017/May/12, Windows no gawk wo sakeru tame
-
-#echo "prog="$prog 1>&2
-
-umask 077
-(
-$prog '
-BEGIN {
-	prefix = ENVIRON["prefix"];
-	version = ENVIRON["version"];
-	myself = ENVIRON["myself"];
-	pwd = ENVIRON["mafft_working_dir"];  # from mafft.bat on windows
-	if( pwd == "" ) pwd = ENVIRON["PWD"];
-	while( 1 )
-	{
-		options = ""
-		printf( "\n" ) > "/dev/tty";
-		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
-		printf( "\n" )                                                                           > "/dev/tty";
-		printf( "   MAFFT %s\n", version )                                                       > "/dev/tty";
-		printf( "\n" )                                                                           > "/dev/tty";
-#		printf( "        Copyright (c) 2002- Kazutaka Katoh\n" )                                 > "/dev/tty";
-		printf( "        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)\n" )                     > "/dev/tty";
-		printf( "        https://mafft.cbrc.jp/alignment/software/\n" )                           > "/dev/tty";
-		printf( "---------------------------------------------------------------------\n" )      > "/dev/tty";
-		printf( "\n" ) > "/dev/tty";
-	
-		while( 1 )
-		{
-			printf( "\n" ) > "/dev/tty";
-			printf( "Input file? (FASTA format; Folder=%s)\n@ ", pwd ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" )
-			if( res == 0 || NF == 0 )
-				continue;
-			infile = sprintf( "%s", $0 );
-	
-			res = getline < infile;
-			close( infile );
-			if( res == -1 )
-			{
-				printf( "%s: No such file.\n\n", infile ) > "/dev/tty";
-				printf( "Filename extension (eg., .txt) must be typed, if any.\n\n" ) > "/dev/tty";
-			}
-			else if( res == 0 )
-				printf( "%s: Empty.\n", infile ) > "/dev/tty";
-			else
-			{
-				printf( "OK. infile = %s\n\n", infile ) > "/dev/tty";
-				break;
-			}
-		}
-		nseq = 0;
-	
-		while( 1 )
-		{
-			printf( "\n" ) > "/dev/tty";
-			printf( "Output file?\n" ) > "/dev/tty";
-			printf( "@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 || NF == 0 )
-				continue;
-			else
-			{
-				outfile = sprintf( "%s", $0 );
-				printf( "OK. outfile = %s\n\n", outfile ) > "/dev/tty";
-				break;
-			}
-		}
-	
-		while( 1 )
-		{
-			outargs = "";
-			printf( "\n" ) > "/dev/tty";
-			printf( "Output format?\n" ) > "/dev/tty";
-			printf( "  1. Clustal format / Sorted\n" ) > "/dev/tty";
-			printf( "  2. Clustal format / Input order\n" ) > "/dev/tty";
-			printf( "  3. Fasta format   / Sorted\n" ) > "/dev/tty";
-			printf( "  4. Fasta format   / Input order\n" ) > "/dev/tty";
-			printf( "  5. Phylip format  / Sorted\n" ) > "/dev/tty";
-			printf( "  6. Phylip format  / Input order\n" ) > "/dev/tty";
-			printf( "@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-#			printf( "res=%d, NF=%d\n", res, NF );
-
-			resnum = 0 + $1;
-#			printf( "resnum=%d\n", resnum );
-
-			if( resnum < 1 || 6 < resnum )
-				continue;
-			else
-			{
-				if( resnum == 1 )
-					outargs = "--clustalout --reorder";
-				else if( resnum == 2 )
-					outargs = "--clustalout --inputorder";
-				else if( resnum == 3 )
-					outargs = "--reorder";
-				else if( resnum == 4 )
-					outargs = "--inputorder";
-				else if( resnum == 5 )
-					outargs = "--phylipout --reorder";
-				else if( resnum == 6 )
-					outargs = "--phylipout --inputorder";
-				else
-					continue;
-				printf( "OK. arguments = %s\n\n", outargs ) > "/dev/tty";
-				break;
-			}
-		}
-	
-		while( 1 )
-		{
-			arguments = "";
-			printf( "\n" ) > "/dev/tty";
-			printf( "Strategy?\n" ) > "/dev/tty";
-			printf( "  1. --auto\n" ) > "/dev/tty";
-			printf( "  2. FFT-NS-1 (fast)\n" ) > "/dev/tty";
-			printf( "  3. FFT-NS-2 (default)\n" ) > "/dev/tty";
-			printf( "  4. G-INS-i  (accurate)\n" ) > "/dev/tty";
-			printf( "  5. L-INS-i  (accurate)\n" ) > "/dev/tty";
-			printf( "  6. E-INS-i  (accurate)\n" ) > "/dev/tty";
-			printf( "@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-#			printf( "res=%d, NF=%d\n", res, NF );
-
-			resnum = 0 + $1;
-#			printf( "resnum=%d\n", resnum );
-
-			if( resnum < 1 || 6 < resnum )
-				continue;
-			else
-			{
-				if( resnum == 1 )
-					arguments = "--auto";
-				else if( resnum == 2 )
-					arguments = "--retree 1";
-				else if( resnum == 3 )
-					arguments = "--retree 2";
-				else if( resnum == 4 )
-					arguments = "--globalpair --maxiterate 16";
-				else if( resnum == 5 )
-					arguments = "--localpair  --maxiterate 16";
-				else if( resnum == 6 )
-					arguments = "--genafpair  --maxiterate 16";
-				else
-					arguments = sprintf( "%s", $0 );
-				printf( "OK. arguments = %s %s\n\n", arguments, outargs ) > "/dev/tty";
-				break;
-			}
-		}
-
-
-		while( 1 )
-		{
-			printf( "\n" ) > "/dev/tty";
-			printf( "Additional arguments? (--ep # --op # --kappa # etc)\n" ) > "/dev/tty";
-			printf( "@ " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 || NF == 0 )
-			{
-				break;
-			}
-			else
-			{
-				addargs = sprintf( "%s", $0 );
-				printf( "OK. arguments = %s %s %s\n\n", addargs, arguments, outargs ) > "/dev/tty";
-				break;
-			}
-		}
-
-		arguments = sprintf( "%s %s %s", addargs, arguments, outargs );
-
-		print ""
-		command = sprintf( "\"%s\" %s \"%s\" > \"%s\"", myself, arguments, infile, outfile );
-		gsub( /\\/, "/", command );
-
-
-		printf( "command=\n%s\n", command ) > "/dev/tty";
-	
-	
-		while( 1 )
-		{
-			go = 0;
-			printf( "OK?\n" ) > "/dev/tty";
-			printf( "@ [Y] " ) > "/dev/tty";
-			res = getline < "/dev/tty";
-			close( "/dev/tty" );
-			if( res == 0 )
-				continue;
-			else if( NF == 0 || $0 ~ /^[Yy]/ )
-			{
-				go=1;
-				break;
-			}
-			else
-				break;
-		}
-		if( go ) break;
-		printf( "\n" ) > "/dev/tty";
-		printf( "\n" ) > "/dev/tty";
-	}
-	system( command );
-	command = sprintf( "more \"%s\"", outfile );
-	system( command );
-	printf( "Press Enter to exit." ) > "/dev/tty";
-	res = getline < "/dev/tty";
-}
-'
-)
-exit 0;
diff --git a/software/mafft/mafft-win/usr/bin/mafft-homologs.rb b/software/mafft/mafft-win/usr/bin/mafft-homologs.rb
deleted file mode 100755
index 3a62cc4d..00000000
--- a/software/mafft/mafft-win/usr/bin/mafft-homologs.rb
+++ /dev/null
@@ -1,505 +0,0 @@
-#!/usr/bin/env ruby
-
-localdb = "sp"
-# database name from which homologues are collected
-# by locally installed blast. Leave this if you do
-# not use the '-l' option.
-
-mafftpath = "/usr/local/bin/mafft"   
-# path of mafft. "/usr/local/bin/mafft"
-# if mafft is in your command path, "mafft" is ok.
-
-blastpath = "psiblast"
-# path of blastall.
-# if blastall is in your command path, "blastall" is ok.
-
-# mafft-homologs.rb  v. 2.1 aligns sequences together with homologues
-# automatically collected from SwissProt via NCBI BLAST.
-#
-# mafft > 5.58 is required
-#
-# Usage:
-#   mafft-homologs.rb [options] input > output
-# Options:
-#   -a #      the number of collected sequences (default: 50)
-#   -e #      threshold value (default: 1e-10)
-#   -o "xxx"  options for mafft
-#             (default: " --op 1.53 --ep 0.123 --maxiterate 1000")
-#   -l        locally carries out blast searches instead of NCBI blast
-#             (requires locally installed blast and a database)
-#   -f        outputs collected homologues also (default: off)
-#   -w        entire sequences are subjected to BLAST search
-#             (default: well-aligned region only)
-
-#require 'getopts'
-require 'optparse'
-require 'tempfile'
-
-if ENV["MAFFT_BLAST"] && ENV["MAFFT_BLAST"] != "" then
-	blastpath = ENV["MAFFT_BLAST"]
-end
-
-if ENV["MAFFT_HOMOLOGS_MAFFT"] && ENV["MAFFT_HOMOLOGS_MAFFT"] != "" then
-	mafftpath = ENV["MAFFT_HOMOLOGS_MAFFT"]
-end
-
-# mktemp
-GC.disable
-temp_vf = Tempfile.new("_vf").path
-temp_if = Tempfile.new("_if").path
-temp_pf = Tempfile.new("_pf").path
-temp_af = Tempfile.new("_af").path
-temp_qf = Tempfile.new("_qf").path
-temp_bf = Tempfile.new("_bf").path
-temp_rid = Tempfile.new("_rid").path
-temp_res = Tempfile.new("_res").path
-
-
-system( mafftpath + " --help > #{temp_vf} 2>&1" )
-pfp = File.open( "#{temp_vf}", 'r' )
-while pfp.gets
-	break if $_ =~ /MAFFT v/
-end
-pfp.close
-
-if( $_ ) then
-	mafftversion = $_.sub( /^\D*/, "" ).split(" ").slice(0).strip.to_s
-else
-	mafftversion = "0"
-end
-if( mafftversion < "5.58" ) then
-	STDERR.puts ""
-	STDERR.puts "======================================================"
-	STDERR.puts "Install new mafft (v. >= 5.58)"
-	STDERR.puts "======================================================"
-	STDERR.puts ""
-	exit
-end
-
-srand ( 0 )
-
-def readfasta( fp, name, seq )
-	nseq = 0
-	tmpseq = ""
-	while fp.gets
-		if $_ =~ /^>/ then
-			name.push( $_.sub(/>/,"").strip )
-			seq.push( tmpseq ) if nseq > 0
-			nseq += 1
-			tmpseq = ""
-		else
-			tmpseq += $_.strip
-		end
-	end
-	seq.push( tmpseq )
-	return nseq
-end
-
-nadd = 600
-num_alignments = 600
-num_threads_blast = 4
-eval = 1e-1
-local = 0
-fullout = 0
-entiresearch = 1
-corewin = 50
-corethr = 0.3
-#mafftopt = " --op 1.53 --ep 0.123 --localpair --maxiterate 1000 --reorder "
-mafftopt = " --op 1.53 --ep 0.0 --globalpair --maxiterate 1000 --reorder "
-
-
-#if getopts( "s", "f", "w", "l", "h", "e:", "a:", "o:", "c:", "d:" ) == nil ||  ARGV.length == 0 || $OPT_h then
-#	puts "Usage: #{$0} [-h -l -e# -a# -o\"[options for mafft]\"] input_file"
-#	exit
-#end
-params = ARGV.getopts( "sfwlhe:a:o:c:d:n:N:" )
-
-
-#if $OPT_c then
-if params["c"] != nil then
-	corewin = params["c"].to_i
-end
-
-#if $OPT_d then
-#if params["d"] != nil then
-#	corethr = params["d"].to_f
-#end
-#
-if params["d"] != nil then
-	localdb = params["d"].to_s
-end
-
-if params["n"] != nil then
-	num_alignments = params["n"].to_s
-end
-
-if params["N"] != nil then
-	num_threads_blast = params["N"].to_s
-end
-
-#if $OPT_w
-if params["w"] == true then
-	entiresearch = 1
-end
-
-#if $OPT_f
-if params["f"] == true then
-	fullout = 1
-end
-
-#if $OPT_s
-if params["s"] == true then
-	fullout = 0
-end
-
-#if $OPT_l
-if params["l"] == true then
-	local = 1
-end
-
-#if $OPT_e then
-if params["e"] != nil then
-#	eval = $OPT_e.to_f
-	eval = params["e"].to_f
-end
-
-#if $OPT_a then
-if params["a"] != nil then
-	nadd = params["a"].to_i
-end
-
-#if $OPT_o then
-if params["o"] != nil then
-	mafftopt += " " + params["o"] + " "
-end
-
-infn = ARGV[0].to_s.strip
-
-system "cat " + infn + " > #{temp_if}"
-ar = mafftopt.split(" ")
-nar = ar.length
-for i in 0..(nar-1)
-	if ar[i] == "--seed" then
-		system "cat #{ar[i+1]} >> #{temp_if}"
-	end
-end
-
-if fullout == 0 then
-	mafftopt += " --excludehomologs "
-end
-
-nseq = 0
-ifp = File.open( "#{temp_if}", 'r' )
-	while ifp.gets
-		nseq += 1 if $_ =~ /^>/
-	end
-ifp.close
-
-if nseq >= 10000 then
-	STDERR.puts "The number of input sequences must be <10000."
-	exit
-elsif nseq == 1 then
-	system( "cp #{temp_if}"  + " #{temp_pf}" )
-else
-	STDERR.puts "Performing preliminary alignment .. "
-	if entiresearch == 1 then
-#		system( mafftpath + " --maxiterate 1000 --localpair #{temp_if} > #{temp_pf}" )
-		system( mafftpath + " --maxiterate 0 --retree 2 #{temp_if} > #{temp_pf}" )
-	else
-		system( mafftpath + " --maxiterate 1000 --localpair --core --coreext --corethr #{corethr.to_s} --corewin #{corewin.to_s} #{temp_if} > #{temp_pf}" )
-	end
-end
-
-pfp = File.open( "#{temp_pf}", 'r' )
-inname = []
-inseq = []
-slen = []
-act = []
-nin = 0
-nin = readfasta( pfp, inname, inseq )
-for i in 0..(nin-1)
-	slen.push( inseq[i].gsub(/-/,"").length )
-	act.push( 1 )
-end
-pfp.close
-
-pfp = File.open( "#{temp_if}", 'r' )
-orname = []
-orseq = []
-nin = 0
-nin = readfasta( pfp, orname, orseq )
-pfp.close
-
-allen = inseq[0].length
-for i in 0..(nin-2)
-	for j in (i+1)..(nin-1)
-		next if act[i] == 0
-		next if act[j] == 0
-		pid = 0.0
-		total = 0
-		for a in 0..(allen-1)
-			next if inseq[i][a,1] == "-" || inseq[j][a,1] == "-"
-			total += 1
-			pid += 1.0 if inseq[i][a,1] == inseq[j][a,1]
-		end
-		pid /= total
-#		puts "#{i.to_s}, #{j.to_s}, #{pid.to_s}"
-		if pid > 0.5 then
-			if slen[i] < slen[j]
-				act[i] = 0
-			else
-				act[j] = 0
-			end
-		end
-	end
-end
-#p act
-
-
-afp = File.open( "#{temp_af}", 'w' )
-
-STDERR.puts "Searching .. \n"
-ids = []
-add = []
-sco = []
-nblast = 0 # ato de tsukau kamo
-for i in 0..(nin-1)
-	singleids = []
-	singleadd = []
-
-	inseq[i].gsub!(/-/,"")
-	afp.puts ">" + orname[i]
-	afp.puts orseq[i]
-
-#	afp.puts ">" + inname[i]
-#	afp.puts inseq[i]
-
-	STDERR.puts "Query (#{i+1}/#{nin})\n" + inname[i]
-	if act[i] == 0 then
-		STDERR.puts "Skip.\n\n"
-		next
-	end
-
-	if local == 0 then
-		command = "lynx -source 'https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=" + inseq[i] + "&DATABASE=swissprot&HITLIST_SIZE=" + nadd.to_s + "&FILTER=L&EXPECT='" + eval.to_s + "'&FORMAT_TYPE=TEXT&PROGRAM=blastp&SERVICE=plain&NCBI_GI=on&PAGE=Proteins&CMD=Put' > #{temp_rid}"
-		system command
-
-		ridp = File.open( "#{temp_rid}", 'r' )
-		while ridp.gets
-			break if $_ =~ / RID = (.*)/
-		end
-		ridp.close
-		rid = $1.strip
-		STDERR.puts "Submitted to NCBI. rid = " + rid
-
-		STDERR.printf "Waiting "
-		while 1
-			STDERR.printf "."
-			sleep 10
-			command = "lynx -source 'https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?RID=" + rid + "&DESCRIPTIONS=500&ALIGNMENTS=" + nadd.to_s + "&ALIGNMENT_TYPE=Pairwise&OVERVIEW=no&CMD=Get&FORMAT_TYPE=XML' > #{temp_res}"
-			system command
-			resp = File.open( "#{temp_res}", 'r' )
-#			resp.gets
-#			if $_ =~ /WAITING/ then
-#				resp.close
-#				next
-#			end
-			while( resp.gets )
-				break if $_ =~ /QBlastInfoBegin/
-			end
-			resp.gets
-			if $_ =~ /WAITING/ then
-				resp.close
-				next
-			else
-				resp.close
-				break
-			end
-		end
-	else
-#		puts "Not supported"
-#		exit
-		qfp = File.open( "#{temp_qf}", 'w' )
-			qfp.puts "> "
-			qfp.puts inseq[i]
-		qfp.close
-		command = blastpath + " -num_iterations 2 -num_threads #{num_threads_blast} -evalue  #{eval} -num_alignments #{num_alignments} -outfmt 5 -query #{temp_qf} -db #{localdb} > #{temp_res}"
-		system command
-#		system "cp #{temp_res} _res"
-	end
-	STDERR.puts " Done.\n\n"
-
-	resp = File.open( "#{temp_res}", 'r' )
-	hitnum = 0
-	lasteval = "nohit"
-
-	while resp.gets
-		break if $_ =~ /2<\/Iteration_iter-num>/
-	end
-
-	if $_ == nil then
-		STDERR.puts "no hit"
-	else
-		while 1
-			while resp.gets
-				break if $_ =~ /(.*)<\/Hit_id>/ || $_ =~ /()/
-			end
-			id = $1
-			break if $_ =~ //
-	#		p id
-
-			starthit = 9999999
-			endhit = -1
-			startquery = 9999999
-			endquery = -1
-			target = ""
-			score = 0.0
-
-			while line = resp.gets
-				if line =~ /(.*)<\/Hsp_hit-from>/
-					starthitcand=$1.to_i
-				elsif line =~ /(.*)<\/Hsp_hit-to>/
-					endhitcand=$1.to_i
-				elsif line =~ /(.*)<\/Hsp_query-from>/
-					startquerycand=$1.to_i
-				elsif line =~ /(.*)<\/Hsp_query-to>/
-					endquerycand=$1.to_i
-				elsif $_ =~ /(.*)<\/Hsp_hseq>/
-					targetcand = $1.sub( /-/, "" ).sub( /U/, "X" )
-				elsif line =~ /(.*)<\/Hsp_bit-score>/
-					scorecand=$1.to_f
-				elsif line =~ /(.*)<\/Hsp_evalue>/
-					evalcand=$1.to_s
-				elsif line =~ /<\/Hsp>/
-					if endhit == -1 then
-						starthit = starthitcand
-						endhit= endhitcand
-						startquery = startquerycand
-						endquery= endquerycand
-						target = targetcand
-						score = scorecand
-						lasteval = evalcand
-					else
-	#					if endhit <=   endhitcand && endquery <=   endquerycand  then
-						if endhit <= starthitcand && endquery <= startquerycand  then
-							endhit = endhitcand
-							endquery = endquerycand
-							target = target + "XX" + targetcand
-							score = score + scorecand
-						end
-	#					if starthitcand <= starthit && startquerycand <= startquery  then
-						if   endhitcand <= starthit &&   endquerycand <= startquery  then
-							starthit = starthitcand
-							startquery = startquerycand
-							target = targetcand + "XX" + target
-							score = score + scorecand
-						end
-					end
-				elsif line =~ /<\/Hit>/
-					hitnum = hitnum + 1
-					break;
-				end
-			end
-
-			singleids.push( id )
-			singleadd.push( target )
-
-			known = ids.index( id )
-			if known != nil then
-				if sco[known] >= score then
-					next
-				else
-					ids.delete_at( known )
-					add.delete_at( known )
-					sco.delete_at( known )
-				end
-			end
-			ids.push( id )
-			sco.push( score )
-			add.push( target )
-
-		end
-		resp.close
-	end
-
-	n = singleids.length
-	outnum = 0
-
-	totalprob = 0
-	prob = []
-	for m in 0..(n-1)
-#		prob[m] = 1.0 / population[eclass[m]]
-		prob[m] = 1.0
-		totalprob += prob[m]
-	end
-#	puts ""
-	for m in 0..(n-1)
-		prob[m] /= (totalprob)
-		prob[m] *= (nadd.to_f / nin.to_f)
-		prob[m] = 1 if prob[m] > 1
-	end
-
-
-	for m in 0..(n-1)
-		if rand( 1000000 ).to_f/1000000 < prob[m] then
-#			STDERR.puts "hit in " + m.to_s
-			afp.puts ">_addedbymaffte_" + singleids[m]
-			afp.puts singleadd[m]
-		end
-	end
-end
-afp.close
-
-STDERR.puts "Aligning .. "
-system( mafftpath + mafftopt + "#{temp_af} > #{temp_bf}" )
-STDERR.puts "done."
-
-bfp = File.open( "#{temp_bf}", 'r' )
-outseq = []
-outnam = []
-readfasta( bfp, outnam, outseq )
-bfp.close
-
-outseq2 = []
-outnam2 = []
-
-len = outseq.length
-for i in 0..(len-1)
-#	p outnam[i]
-	if fullout == 0 && outnam[i] =~ /_addedbymaffte_/ then
-		next
-	end
-	outseq2.push( outseq[i] )
-	outnam2.push( outnam[i].sub( /_addedbymaffte_/, "_ho_" ) )
-end
-
-nout = outseq2.length
-len = outseq[0].length
-p = len
-while p>0
-	p -= 1
-    allgap = 1
-    for j in 0..(nout-1)
-		if outseq2[j][p,1] != "-" then
-			allgap = 0
-			break
-		end
-    end
-    if allgap == 1 then
-        for j in 0..(nout-1)
-            outseq2[j][p,1] = ""
-        end
-    end
-end
-for i in 0..(nout-1)
-	puts ">" + outnam2[i]
-	puts outseq2[i].gsub( /.{1,60}/, "\\0\n" )
-end
-
-
-system( "rm -rf #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid}" )
-#system( "cp #{temp_if} #{temp_vf} #{temp_af} #{temp_bf} #{temp_pf} #{temp_qf} #{temp_res} #{temp_rid} ." )
-if File.exist?( "#{temp_af}.tree" ) then
-	system( "sed 's/_addedbymaffte_/_ho_/'  #{temp_af}.tree > #{ARGV[0].to_s}.tree" )
-	system( "rm #{temp_af}.tree" )
-end
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diff --git a/software/mafft/mafft-win/usr/lib/mafft/mafft-homologs.1 b/software/mafft/mafft-win/usr/lib/mafft/mafft-homologs.1
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--- a/software/mafft/mafft-win/usr/lib/mafft/mafft-homologs.1
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@@ -1,131 +0,0 @@
-.\"     Title: MAFFT-HOMOLOGS
-.\"    Author: Kazutaka Katoh 
-.\" Generator: DocBook XSL Stylesheets v1.72.0 
-.\"      Date: 2007-08-14
-.\"    Manual: Mafft Manual
-.\"    Source: mafft-homologs 2.1
-.\"
-.TH "MAFFT\-HOMOLOGS" "1" "2007\-06\-09" "mafft\-homologs 2.1" "Mafft Manual"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "NAME"
-.RS 0
-mafft\-homologs \- aligns sequences together with homologues automatically collected from SwissProt via NCBI BLAST
-.RE
-.SH "SYNOPSIS"
-.RS 0
-\fBmafft\-homologs\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.SH "DESCRIPTION"
-.RS 0
-The accuracy of an alignment of a few distantly related sequences is considerably improved when being aligned together with their close homologs. The reason for the improvement is probably the same as that for PSI\-BLAST. That is, the positions of highly conserved residues, those with many gaps and other additional information is brought by close homologs. According to Katoh et al. (2005), the improvement by adding close homologs is 10% or so, which is comparable to the improvement by incorporating structural information of a pair of sequences. Mafft\-homologs in a mafft server works like this:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Collect a number (50 by default) of close homologs (E=1e\-10 by default) of the input sequences.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Align the input sequences and homologs all together using the L\-INS\-i strategy.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'Remove the homologs.
-.RE
-.RE
-.SH "OPTIONS"
-.RS 0
-.PP
-\fB\-a\fR \fI\fIn\fR\fR
-.RS 4
-The number of collected sequences (default: 50).
-.RE
-.PP
-\fB\-e\fR \fI\fIn\fR\fR
-.RS 4
-Threshold value (default: 1e\-10).
-.RE
-.PP
-\fB\-o\fR \fI\fIxxx\fR\fR
-.RS 4
-Options for mafft (default: " \-\-op 1.53 \-\-ep 0.123 \-\-maxiterate 1000 --localpair --reorder").
-.RE
-.PP
-\fB\-l\fR
-.RS 4
-Locally carries out BLAST searches instead of NCBI BLAST (requires locally installed BLAST and a database).
-.RE
-.PP
-\fB\-f\fR
-.RS 4
-Outputs collected homologues also (default: off).
-.RE
-.PP
-\fB\-w\fR
-.RS 4
-entire sequences are subjected to BLAST search (default: well\-aligned region only)
-.RE
-.RE
-.SH "REQUIREMENTS"
-.RS 0
-.PP
-MAFFT version > 5.58.
-.PP
-Either of
-.RS 4
-.PP
-lynx (when remote BLAST server is used)
-.PP
-BLAST and a protein sequence database (when local BLAST is used)
-.RE
-.RE
-.SH "REFERENCES"
-.RS 0
-.PP
-Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment.
-.RE
-.SH "SEE ALSO"
-.RS 0
-.PP
-\fBmafft\fR(1)
-.RE
-.SH "AUTHORS"
-.RS 0
-.PP
-\fBKazutaka Katoh\fR <\&katoh_at_bioreg.kyushu\-u.ac.jp.\&>
-.sp -1n
-.IP "" 4
-Wrote Mafft.
-.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam@plessy.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
-.RE
-.SH "COPYRIGHT"
-.RS 0
-Copyright \(co 2002\-2007 Kazutaka Katoh (mafft)
-.br
-Copyright \(co 2007 Charles Plessy (this manpage)
-.br
-.PP
-Mafft and its manpage are offered under the following conditions:
-.PP
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.
-.RE
-.PP
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-.br
-.RE
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--- a/software/mafft/mafft-win/usr/lib/mafft/mafft.1
+++ /dev/null
@@ -1,479 +0,0 @@
-.\"     Title: MAFFT
-.\"    Author: Kazutaka Katoh 
-.\" Generator: DocBook XSL Stylesheets v1.72.0 
-.\"      Date: 2007-08-14
-.\"    Manual: Mafft Manual
-.\"    Source: mafft 6.240
-.\"
-.TH "MAFFT" "1" "2007\-06\-09" "mafft 6.240" "Mafft Manual"
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.SH "THIS MANUAL IS FOR V6.2XX (2007)"
-Recent versions (v7.1xx; 2013 Jan.) have more features than those described below.
-See also the tips page at 
-http://mafft.cbrc.jp/alignment/software/tips0.html
-.SH "NAME"
-.RS 0
-.sp
-mafft \- Multiple alignment program for amino acid or nucleotide sequences
-.RE
-.SH "SYNOPSIS"
-.RS 0
-.HP 6
-\fBmafft\fR [\fBoptions\fR] \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 7
-\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 5
-\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 14
-\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
-.HP
-.sp
-\fIinput\fR, \fIgroup1\fR and \fIgroup2\fR must be in FASTA format.
-.RE
-.SH "DESCRIPTION"
-.RS 0
-\fBMAFFT\fR is a multiple sequence alignment program for unix\-like operating systems. It offers a range of multiple alignment methods.
-.SS "Accuracy\-oriented methods:"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'L\-INS\-i (probably most accurate; recommended for <200 sequences; iterative refinement method incorporating local pairwise alignment information):
-.HP 6
-\fBmafft\fR \fB\-\-localpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBlinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'G\-INS\-i (suitable for sequences of similar lengths; recommended for <200 sequences; iterative refinement method incorporating global pairwise alignment information):
-.HP 6
-\fBmafft\fR \fB\-\-globalpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBginsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'E\-INS\-i (suitable for sequences containing large unalignable regions; recommended for <200 sequences):
-.HP 6
-\fBmafft\fR \fB\-\-ep\fR\ \fI0\fR \fB\-\-genafpair\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBeinsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.br
-
-For E\-INS\-i, the
-\fB\-\-ep\fR
-\fI0\fR
-option is recommended to allow large gaps.
-.RE
-.SS "Speed\-oriented methods:"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; two cycles only):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 7
-\fBfftnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-i (iterative refinement method; max. 1000 iterations):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-2 (fast; progressive method):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBfftns\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'FFT\-NS\-1 (very fast; recommended for >2000 sequences; progressive method with a rough guide tree):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'NW\-NS\-i (iterative refinement method without FFT approximation; two cycles only):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI2\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR]
-.HP 7
-\fBnwnsi\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'NW\-NS\-2 (fast; progressive method without the FFT approximation):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI2\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fIinput\fR [>\ \fIoutput\fR]
-.HP 6
-\fBnwns\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'NW\-NS\-PartTree\-1 (recommended for ~10,000 to ~50,000 sequences; progressive method with the PartTree algorithm):
-.HP 6
-\fBmafft\fR \fB\-\-retree\fR\ \fI1\fR \fB\-\-maxiterate\fR\ \fI0\fR \fB\-\-nofft\fR\ \fB\-\-parttree\fR \fIinput\fR [>\ \fIoutput\fR]
-.RE
-.SS "Group\-to\-group alignments"
-.HP 6
-.RS 4
-\fBmafft\-profile\fR \fIgroup1\fR \fIgroup2\fR [>\ \fIoutput\fR]
-.sp
-or:
-.sp
-\fBmafft\fR \fB\-\-maxiterate\fR\ \fI1000\fR \fB\-\-seed\fR\ \fIgroup1\fR \fB\-\-seed\fR\ \fIgroup2\fR /dev/null [>\ \fIoutput\fR]
-.RE
-.RE
-.RE
-.SH "OPTIONS"
-.SS "Algorithm"
-.RS 0
-.PP
-\fB\-\-auto\fR
-.RS 4
-Automatically selects an appropriate strategy from L\-INS\-i, FFT\-NS\-i and FFT\-NS\-2, according to data 
-size.  Default: off (always FFT\-NS\-2)
-.RE
-.PP
-\fB\-\-6merpair\fR
-.RS 4
-Distance is calculated based on the number of shared 6mers.  Default: on
-.RE
-.PP
-\fB\-\-globalpair\fR
-.RS 4
-All pairwise alignments are computed with the Needleman\-Wunsch
-algorithm.  More accurate but slower 
-than \-\-6merpair.  Suitable for a set of
-globally alignable sequences.  Applicable to 
-up to ~200 sequences.  A combination with \-\-maxiterate 1000 is recommended (G\-INS\-i).  Default: off (6mer distance is used)
-.RE
-.PP
-\fB\-\-localpair\fR
-.RS 4
-All pairwise alignments are computed with the Smith\-Waterman
-algorithm.  More accurate but slower
-than \-\-6merpair.  Suitable for a set of 
-locally alignable sequences.  Applicable to 
-up to ~200 sequences.  A combination with \-\-maxiterate 1000 is recommended (L\-INS\-i).  Default: off (6mer distance is used)
-.RE
-.PP
-\fB\-\-genafpair\fR
-.RS 4
-All pairwise alignments are computed with a local
-algorithm with the generalized affine gap cost
-(Altschul 1998).  More accurate but slower
-than \-\-6merpair.  Suitable when large internal gaps
-are expected.  Applicable to 
-up to ~200 sequences.  A combination with \-\-maxiterate 1000 is recommended (E\-INS\-i).  Default: off (6mer distance is used)
-.RE
-.\".PP
-.\"\fB\-\-fastswpair\fR
-.\".RS 4
-.\"Distance is calculated based on a FASTA alignment. 
-.\"FASTA is required.  Default: off (6mer distance is used)
-.\".RE
-.PP
-\fB\-\-fastapair\fR
-.RS 4
-All pairwise alignments are computed with FASTA (Pearson and Lipman 1988).
-FASTA is required.  Default: off (6mer distance is used)
-.RE
-.\".PP
-.\"\fB\-\-blastpair\fR
-.\".RS 4
-.\"Distance is calculated based on a BLAST alignment.  BLAST is 
-.\"required.  Default: off (6mer distance is used)
-.\".RE
-.PP
-\fB\-\-weighti\fR \fInumber\fR
-.RS 4
-Weighting factor for the consistency term calculated from pairwise alignments.  Valid when 
-either of \-\-globalpair, \-\-localpair,  \-\-genafpair, \-\-fastapair or 
-\-\-blastpair is selected.  Default: 2.7
-.RE
-.PP
-\fB\-\-retree\fR \fInumber\fR
-.RS 4
-Guide tree is built \fInumber\fR times in the 
-progressive stage.  Valid with 6mer distance.  Default: 2
-.RE
-.PP
-\fB\-\-maxiterate\fR \fInumber\fR
-.RS 4
-\fInumber\fR cycles of iterative refinement are performed.  Default: 0
-.RE
-.PP
-\fB\-\-fft\fR
-.RS 4
-Use FFT approximation in group\-to\-group alignment.  Default: on
-.RE
-.PP
-\fB\-\-nofft\fR
-.RS 4
-Do not use FFT approximation in group\-to\-group alignment.  Default: off
-.RE
-.PP
-\fB\-\-noscore\fR
-.RS 4
-Alignment score is not checked in the iterative refinement stage.  Default: off (score is checked)
-.RE
-.PP
-\fB\-\-memsave\fR
-.RS 4
-Use the Myers\-Miller (1988) algorithm.  Default: automatically turned on when the alignment length exceeds 10,000 (aa/nt).
-.RE
-.PP
-\fB\-\-parttree\fR
-.RS 4
-Use a fast tree\-building method (PartTree, Katoh and Toh 2007) with
-the 6mer distance.  Recommended for a large number (> ~10,000) 
-of sequences are input.  Default: off
-.RE
-.PP
-\fB\-\-dpparttree\fR
-.RS 4
-The PartTree algorithm is used with distances based on DP.  Slightly
-more accurate and slower than \-\-parttree.  Recommended for a large
-number (> ~10,000) of sequences are input.   Default: off
-.RE
-.PP
-\fB\-\-fastaparttree\fR
-.RS 4
-The PartTree algorithm is used with distances based on FASTA.  Slightly more accurate and slower than \-\-parttree.  Recommended for a large number (> ~10,000) of sequences are input.  FASTA is required.  Default: off
-.RE
-.PP
-\fB\-\-partsize\fR \fInumber\fR
-.RS 4
-The number of partitions in the PartTree algorithm.  Default: 50
-.RE
-.PP
-\fB\-\-groupsize\fR \fInumber\fR
-.RS 4
-Do not make alignment larger than \fInumber\fR sequences. Valid only with the \-\-*parttree options.  Default: the number of input sequences
-.RE
-.RE
-.SS "Parameter"
-.RS 0
-.PP
-\fB\-\-op\fR \fInumber\fR
-.RS 4
-Gap opening penalty at group\-to\-group alignment.  Default: 1.53
-.RE
-.PP
-\fB\-\-ep\fR \fInumber\fR
-.RS 4
-Offset value, which works like gap extension penalty, for
-group\-to\-group alignment.  Default: 0.123
-.RE
-.PP
-\fB\-\-lop\fR \fInumber\fR
-.RS 4
-Gap opening penalty at local pairwise 
-alignment.  Valid when
-the \-\-localpair or \-\-genafpair option is selected.  Default: \-2.00
-.RE
-.PP
-\fB\-\-lep\fR \fInumber\fR
-.RS 4
-Offset value at local pairwise alignment.  Valid when
-the \-\-localpair or \-\-genafpair option is selected.  Default: 0.1
-.RE
-.PP
-\fB\-\-lexp\fR \fInumber\fR
-.RS 4
-Gap extension penalty at local pairwise alignment.  Valid when
-the \-\-localpair or \-\-genafpair option is selected.  Default: \-0.1
-.RE
-.PP
-\fB\-\-LOP\fR \fInumber\fR
-.RS 4
-Gap opening penalty to skip the alignment.  Valid when the
-\-\-genafpair option is selected.   Default: \-6.00
-.RE
-.PP
-\fB\-\-LEXP\fR \fInumber\fR
-.RS 4
-Gap extension penalty to skip the alignment.  Valid when the
-\-\-genafpair option is selected.   Default: 0.00
-.RE
-.PP
-\fB\-\-bl\fR \fInumber\fR
-.RS 4
-BLOSUM \fInumber\fR matrix (Henikoff and Henikoff 1992) is used.  \fInumber\fR=30, 45, 62 or 80.  Default: 62
-.RE
-.PP
-\fB\-\-jtt\fR \fInumber\fR
-.RS 4
-JTT PAM \fInumber\fR (Jones et al. 1992) matrix is used.  \fInumber\fR>0.  Default: BLOSUM62
-.RE
-.PP
-\fB\-\-tm\fR \fInumber\fR
-.RS 4
-Transmembrane PAM \fInumber\fR (Jones et al. 1994) matrix is used.  \fInumber\fR>0.  Default: BLOSUM62
-.RE
-.PP
-\fB\-\-aamatrix\fR \fImatrixfile\fR
-.RS 4
-Use a user\-defined AA scoring matrix.  The format of \fImatrixfile\fR is
-the same to that of BLAST.  Ignored when nucleotide sequences are input.   Default: BLOSUM62
-.RE
-.PP
-\fB\-\-fmodel\fR
-.RS 4
-Incorporate the AA/nuc composition information into
-the scoring matrix.  Default: off
-.RE
-.RE
-.SS "Output"
-.RS 0
-.PP
-\fB\-\-clustalout\fR
-.RS 4
-Output format: clustal format.  Default: off (fasta format)
-.RE
-.PP
-\fB\-\-inputorder\fR
-.RS 4
-Output order: same as input.  Default: on
-.RE
-.PP
-\fB\-\-reorder\fR
-.RS 4
-Output order: aligned.  Default: off (inputorder)
-.RE
-.PP
-\fB\-\-treeout\fR
-.RS 4
-Guide tree is output to the \fIinput\fR.tree file.  Default: off
-.RE
-.PP
-\fB\-\-quiet\fR
-.RS 4
-Do not report progress.  Default: off
-.RE
-.RE
-.SS "Input"
-.RS 0
-.PP
-\fB\-\-nuc\fR
-.RS 4
-Assume the sequences are nucleotide.  Default: auto
-.RE
-.PP
-\fB\-\-amino\fR
-.RS 4
-Assume the sequences are amino acid.  Default: auto
-.RE
-.PP
-\fB\-\-seed\fR \fIalignment1\fR [\fB--seed\fR \fIalignment2\fR \fB--seed\fR \fIalignment3\fR ...]
-.RS 4
-Seed alignments given in \fIalignment_n\fR (fasta format) are aligned with 
-sequences in \fIinput\fR.  The alignment within every seed is preserved.
-.RE
-.RE
-.SH "FILES"
-.RS 0
-.PP
-Mafft stores the input sequences and other files in a temporary directory, which by default is located in
-\fI/tmp\fR.
-.RE
-.SH "ENVIONMENT"
-.RS 0
-.PP
-\fBMAFFT_BINARIES\fR
-.RS 4
-Indicates the location of the binary files used by mafft. By default, they are searched in
-\fI/usr/local/lib/mafft\fR, but on Debian systems, they are searched in
-\fI/usr/lib/mafft\fR.
-.RE
-.PP
-\fBFASTA_4_MAFFT\fR
-.RS 4
-This variable can be set to indicate to mafft the location to the fasta34 program if it is not in the PATH.
-.RE
-.RE
-.SH "SEE ALSO"
-.RS 0
-.PP
-
-\fBmafft\-homologs\fR(1)
-.RE
-.SH "REFERENCES"
-.RS 0
-.SS "In English"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Toh (Bioinformatics 23:372\-374, 2007) PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences (describes the PartTree algorithm).
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh, Kuma, Toh and Miyata (Nucleic Acids Res. 33:511\-518, 2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment (describes [ancestral versions of] the G\-INS\-i, L\-INS\-i and E\-INS\-i strategies)
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh, Misawa, Kuma and Miyata (Nucleic Acids Res. 30:3059\-3066, 2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform (describes the FFT\-NS\-1, FFT\-NS\-2 and FFT\-NS\-i strategies)
-.RE
-.SS "In Japanese"
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Misawa (Seibutsubutsuri 46:312\-317, 2006) Multiple Sequence Alignments: the Next Generation
-.RE
-.sp
-.RS 4
-\h'-04'\(bu\h'+03'Katoh and Kuma (Kagaku to Seibutsu 44:102\-108, 2006) Jissen\-teki Multiple Alignment
-.RE
-.RE
-.SH "AUTHORS"
-.RS 0
-.PP
-\fBKazutaka Katoh\fR <\&kazutaka.katoh_at_aist.go.jp\&>
-.sp -1n
-.IP "" 4
-Wrote Mafft.
-.PP
-\fBCharles Plessy\fR <\&charles\-debian\-nospam_at_plessy.org\&>
-.sp -1n
-.IP "" 4
-Wrote this manpage in DocBook XML for the Debian distribution, using Mafft's homepage as a template.
-.RE
-.SH "COPYRIGHT"
-.RS 0
-Copyright \(co 2002\-2007 Kazutaka Katoh (mafft)
-.br
-Copyright \(co 2007 Charles Plessy (this manpage)
-.br
-.PP
-Mafft and its manpage are offered under the following conditions:
-.PP
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
-.sp
-.RS 4
-\h'-04' 1.\h'+02'Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
-.RE
-.sp
-.RS 4
-\h'-04' 2.\h'+02'Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
-.RE
-.sp
-.RS 4
-\h'-04' 3.\h'+02'The name of the author may not be used to endorse or promote products derived from this software without specific prior written permission.
-.RE
-.PP
-THIS SOFTWARE IS PROVIDED BY THE AUTHOR "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-.br
-.RE
diff --git a/software/mafft/mafft-win/usr/lib/mafft/mafftash_premafft.pl b/software/mafft/mafft-win/usr/lib/mafft/mafftash_premafft.pl
deleted file mode 100755
index 6dc3b9c4..00000000
--- a/software/mafft/mafft-win/usr/lib/mafft/mafftash_premafft.pl
+++ /dev/null
@@ -1,464 +0,0 @@
-#!/usr/bin/perl
-
-#####################################################################
-# Author:  KM Amada (kmamada@ifrec.osaka-u.ac.jp)
-#
-# Ver. Date      Changelog
-#####################################################################
-# 1.0  07.26.13  Initial release
-# 2.0  09.03.13  Added extensive warnings and error messages
-# 3.0  10.28.13  Fix for retrieving large files. Added STDERR logs
-# 3.1  11.08.13  Added LWP failsafe. Made hat3 not a required output
-# 3.2  12.08.14  Removed 5-char restriction for own structure files
-#
-#####################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error 'Header line too long (limit is 8192)' [v3.1]
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/MAFFTash/REST/service.cgi/premafft";
-
-my ( $WORKDIR, $PDBLIST, $OWNLIST, $HAT3FILE, $INSTRFILE );
-
-GetOptions
-(
-    'd=s' => \$WORKDIR,
-    'p=s' => \$PDBLIST,
-    'o=s' => \$OWNLIST,
-    'h=s' => \$HAT3FILE,
-    'i=s' => \$INSTRFILE,
-);
-
-print STDERR "[MAFFTash-premafft]\n";
-
-# set temp directory
-my $TMP = "/tmp/mapremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-&help("Required parameter : atleast one of either '-p' or '-o'") unless ( defined $PDBLIST || defined $OWNLIST);
-&help("Required parameter : '-d'") if defined $OWNLIST && ! defined $WORKDIR;
-
-$HAT3FILE = "hat3" unless defined $HAT3FILE;
-$INSTRFILE = "instr" unless defined $INSTRFILE;
-chop $WORKDIR if defined $WORKDIR && $WORKDIR =~ m/\/$/g;
-
-
-######
-# prepare inputs
-print STDERR "Preparing inputs for service request...\n";
-
-my @files = ();
-push(@files, "strweight" => "0.5");
-push(@files, "premafft" => "1");
-
-
-# pdb entries
-if ( defined $PDBLIST )
-{
-    print STDERR "PDB List defined!\n";
-    &bail("Error: Input file $PDBLIST does not exists!") unless -e $PDBLIST;
-    my $listfile = "$TMP/pdblist.inp";
-
-
-    open(INPF,"<$PDBLIST") or &bail("Error: Cannot open file $PDBLIST for reading!");
-    open(OUTF,">$listfile") or &bail("Error: Cannot open temporary file $listfile for writing!");
-
-    while()
-    {
-        chomp;
-        if ( /^(\w{5})$/ )
-        {
-            print OUTF ">PDBID\n$1\n";
-        }
-    }
-
-    close OUTF;
-    close INPF;
-
-    push(@files, "inputfile" => ["$listfile"]);
-}
-
-
-
-# upload own structures
-my %ownids = ();
-
-if ( defined $OWNLIST  )
-{
-    print STDERR "OWN List defined!\n";
-    &bail("Error: Input file $OWNLIST does not exists!") unless -e $OWNLIST;
-
-
-    open(OWNINPF,"<$OWNLIST") or &bail("Error: Cannot open file $OWNLIST for reading!");
-
-    while()
-    {
-        chomp;
-
-        if ( /^(\S+)$/ )
-        {
-            my $fileref = "$WORKDIR/$1.pdb";
-
-            unless (-e $fileref)
-            {
-                close OWNINPF;
-                &bail("Error: File $fileref does not exists!");
-            }
-
-            push(@files, "inputownfile[]" => ["$fileref"]);
-            $ownids{$1} = 1;
-        }
-    }
-
-    close OWNINPF;
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@files, 'Content_Type' => 'form-data' );
-&bail(sprintf("[%d] %s\n", $postResponse->code, &parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $mafftashid) = &parseResponse($postResponse->content);
-
-
-
-my $MAXTRIES = 3;
-my $STIMER = 4;
-my $longtimer = 0;
-
-print STDERR "Request sent! Waiting for response...[$mafftashid]\n";
-
-
-# wait for results until it becomes available
-while(1)
-{
-    $longtimer = $longtimer <= ($STIMER*3) ? $longtimer+$STIMER : $STIMER;
-    sleep $longtimer;
-
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$mafftashid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $mafftashid) = &parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum.tar.gz";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/getmdlist/$mafftashid", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                my $checklist = &extractchecksum($csfile);
-                &bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( keys %$checklist )
-                {
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$mafftashid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            my $hashid = &getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                unlink $checkfile if -e $checkfile;
-                                &bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            &bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                &bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        &bail(sprintf("[%d] %s\n", $getResponse->code, &parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-&backticks("cat $TMP/archive.tar.gz* | tar -zxf - -C $TMP/");
-&backticks("mv -f $TMP/instr $INSTRFILE") if -e "$TMP/instr";
-&backticks("mv -f $TMP/hat3 $HAT3FILE") if -e "$TMP/hat3";
-
-# sometimes no hat3 file is generated [v3.1]
-#&bail("Error: Output file $HAT3FILE not found!") unless -e $HAT3FILE;
-&bail("Error: Output file $INSTRFILE not found!") unless -e $INSTRFILE;
-
-
-# warn if some ownids were ommitted
-if ( scalar keys(%ownids) > 0 )
-{
-    my %instrids = ();
-
-    open(INSTRF,"<$INSTRFILE") or &bail("Error: Cannot open file $INSTRFILE for reading!");
-
-    while()
-    {
-        chomp;
-
-        if ( /^>\d+_(\S+)$/ )
-        {
-            $instrids{$1} = 1;
-        }
-    }
-
-    close INSTRF;
-
-    foreach my $id ( keys %ownids )
-    {
-        warn "Warning: Own structure $id was excluded from instr/hat3.\n" unless $instrids{$id};
-    }
-
-}
-
-
-
-&cleanup();
-
-
-
-####################
-####################
-
-
-
-sub parseResponse
-{
-    my $response = shift;
-
-    #"status":"wait","mafftashid":"Ma8211432R"
-
-    my $status = "";
-    my $mafftashid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $mafftashid = $1;
-        $status = $2;
-    }
-
-    return ($status, $mafftashid);
-
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-
-    while()
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-
-    }
-
-    close CSUM;
-
-    return \%dataset;
-
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : "";
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while()
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    print STDERR "$str\n" if defined $str;
-
-    &cleanup();
-    exit(1);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./mafftash_premafft.pl -p [FILE]
-  ./mafftash_premafft.pl -o [FILE] -d [DIRECTORY]
-  ./mafftash_premafft.pl -p [FILE] -o [FILE] -d [DIRECTORY]
-
-
-PARAMETERS
-  -p [FILE]
-     FILE contains a list of PDBIDs (one entry per line); make sure that the PDBIDs are in the standard 5-character pdbid+chain naming format
-
-  -o [FILE] -d [DIRECTORY]
-     FILE contains a list of IDs from your own structure/pdb files (one entry per line)
-     for each ID in the list make sure that a corresponding structure file (same ID with .pdb extension) is stored in DIRECTORY
-
-  -h [HATFILE]
-     save the output hat3 file in HATFILE; if not set, the output is written to a file named 'hat3' in your current directory
-
-  -i [INSTRFILE]
-     save the output instr file in INSTRFILE; if not set, the output is written to a file named 'instr' in your current directory
-
-HELPME
-
-    &bail($str);
-}
-
-
-
diff --git a/software/mafft/mafft-win/usr/lib/mafft/maffttext2hex.exe b/software/mafft/mafft-win/usr/lib/mafft/maffttext2hex.exe
deleted file mode 100755
index 32309e33..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/maffttext2hex.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/makedirectionlist.exe b/software/mafft/mafft-win/usr/lib/mafft/makedirectionlist.exe
deleted file mode 100755
index bdf916cd..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/makedirectionlist.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/mccaskillwrap.exe b/software/mafft/mafft-win/usr/lib/mafft/mccaskillwrap.exe
deleted file mode 100755
index f7a43b7a..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/mccaskillwrap.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/multi2hat3s.exe b/software/mafft/mafft-win/usr/lib/mafft/multi2hat3s.exe
deleted file mode 100755
index 8084eee3..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/multi2hat3s.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/nodepair.exe b/software/mafft/mafft-win/usr/lib/mafft/nodepair.exe
deleted file mode 100755
index e162841d..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/nodepair.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/pairash.exe b/software/mafft/mafft-win/usr/lib/mafft/pairash.exe
deleted file mode 100755
index 4a2f905f..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/pairash.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/pairlocalalign.exe b/software/mafft/mafft-win/usr/lib/mafft/pairlocalalign.exe
deleted file mode 100755
index f47e1879..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/pairlocalalign.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/regtable2seq.exe b/software/mafft/mafft-win/usr/lib/mafft/regtable2seq.exe
deleted file mode 100755
index 7abd1dc8..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/regtable2seq.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/replaceu.exe b/software/mafft/mafft-win/usr/lib/mafft/replaceu.exe
deleted file mode 100755
index d8548c9e..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/replaceu.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/restoreu.exe b/software/mafft/mafft-win/usr/lib/mafft/restoreu.exe
deleted file mode 100755
index 9adaa482..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/restoreu.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/score.exe b/software/mafft/mafft-win/usr/lib/mafft/score.exe
deleted file mode 100755
index 2b5c7d61..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/score.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/seekquencer_premafft.pl b/software/mafft/mafft-win/usr/lib/mafft/seekquencer_premafft.pl
deleted file mode 100755
index a9040fdd..00000000
--- a/software/mafft/mafft-win/usr/lib/mafft/seekquencer_premafft.pl
+++ /dev/null
@@ -1,600 +0,0 @@
-#!/usr/bin/perl
-
-####################################################################################
-# Author:  KM Amada (kmamada@ifrec.osaka-u.ac.jp)
-#
-# Ver. Date      Changelog
-####################################################################################
-# 1.0  11.01.13  Initial release
-#
-# **Skipped version 2 to standardise version numbers to seekquencer.pl script**
-#
-# 3.0  04.24.14  Added split option -mod  for output
-#                Uses seekquencer_v3 backend
-#
-# 4.0  05.12.14  Added new options: -run  -trd  -noin
-#                Sets -seqa fast in seekquencer.pl
-#                Uses seekquencer_v4 backend
-#
-# 4.1  05.19.14  Added a check on running REST requests before proceeding
-#                to avoid server load problems
-#
-# 4.2  05.27.14  Seq limit processing done in seekquencer.pl script
-#                to avoid server load problems
-#
-# 4.3  07.22.14  Added new option: -seqd 
-#                Blast limit changed from factor of 10 to -blim option
-#                Timing on sleep changed; added srand() for making seed
-#                Moved the job limit processing to server side
-#
-# 4.4  08.05.14  Modified to work in multiple OS
-#
-#
-####################################################################################
-
-use strict;
-use Getopt::Long;
-use File::Path qw(make_path remove_tree);
-use Cwd;
-use LWP::Simple;
-use LWP::UserAgent;
-
-# to prevent error: Header line too long (limit is 8192)
-use LWP::Protocol::http;
-push(@LWP::Protocol::http::EXTRA_SOCK_OPTS, MaxLineLength => 0);
-
-
-
-my $BASEURL = "http://sysimm.ifrec.osaka-u.ac.jp/seekquencer/REST/service.cgi/premafft";
-my ( $INPUTFILE, $IDLISTFILE, $SEQFASTAFILE, $OUTPUTFILE, $SEQFLAG, $STRFLAG, $EVALFLAG, $NOINFLAG );
-my $OUTTYPE = "mafftash";
-
-my $SEQDATABASE = "uniref100";
-my $SEQLIMIT = 100;
-my $SEQBLASTLIMIT = 100;
-
-my $RUNMODE = "normal";    # thread|normal
-my $THREADCOUNT = 3;
-
-
-GetOptions
-(
-    'inp=s'  => \$INPUTFILE,
-    'idf=s'  => \$IDLISTFILE,
-    'seqf=s' => \$SEQFASTAFILE,
-    'out=s'  => \$OUTPUTFILE,
-    'str'    => \$STRFLAG,
-    'seq'    => \$SEQFLAG,
-    'seqd=s' => \$SEQDATABASE,
-    'lim=i'  => \$SEQLIMIT,
-    'blim=i' => \$SEQBLASTLIMIT,
-    'pre'    => \$EVALFLAG,
-    'noin'   => \$NOINFLAG,
-    'mod=s'  => \$OUTTYPE,
-    'run=s'  => \$RUNMODE,
-    'trd=i'  => \$THREADCOUNT,
-
-
-);
-
-my $ISWINDOWS = ( $^O =~ /^MSWin/ ) ? 1 : 0;
-print STDERR "[Seekquencer-premafft 4.4 on $^O]\n";
-
-
-# set temp directory
-my $CWD = getcwd;
-my $TMP = "$CWD/seekpremafft$$";
-make_path($TMP) unless -d $TMP;
-
-
-
-######
-# validation
-help("Required parameter: define input as '-inp' or '-idf' or '-seqf'") if ( !defined $INPUTFILE && !defined $IDLISTFILE && !defined $SEQFASTAFILE );
-help("'-inp' is already defined") if ( defined $INPUTFILE && (defined $IDLISTFILE || defined $SEQFASTAFILE) );
-help("Input file $INPUTFILE does not exist (or filesize is 0)") if ( defined $INPUTFILE && (! -e $INPUTFILE || !-s $INPUTFILE) );
-help("Input file $IDLISTFILE does not exist (or filesize is 0)") if ( defined $IDLISTFILE && (! -e $IDLISTFILE || !-s $IDLISTFILE) );
-help("Input file $SEQFASTAFILE does not exist (or filesize is 0)") if ( defined $SEQFASTAFILE && (! -e $SEQFASTAFILE || !-s $SEQFASTAFILE) );
-help("Required parameter: output file '-out'") unless ( defined $OUTPUTFILE );
-help("Set either '-str' or '-seq' or dont set any at all") if ( defined $STRFLAG && defined $SEQFLAG );
-
-help("Invalid value for '-seqd '") if ( $SEQDATABASE ne "uniref100" && $SEQDATABASE ne "uniref90" && $SEQDATABASE ne "uniref70" && $SEQDATABASE ne "uniprot");
-help("Invalid value for '-mod '") if ( $OUTTYPE ne "fasta" && $OUTTYPE ne "mafftash" && $OUTTYPE ne "mafftash-split" );
-help("Invalid value for '-run '") if ( $RUNMODE ne "thread" && $RUNMODE ne "normal" );
-help("Invalid value for '-trd '; count should be between 1 and 5 (inclusive)") if ( $RUNMODE eq "thread" && ($THREADCOUNT <= 0 || $THREADCOUNT > 5) );
-
-
-######
-# check existing requests
-print STDERR "Checking server status...\n";
-
-# generate seed
-srand($$);
-
-# sleep a bit to give time for lsf response
-sleep(int(rand(6))+1);
-
-
-my $browser = LWP::UserAgent->new;
-$browser->timeout(0);
-
-# get: check if you can send a new request this time
-my $jobsResponse = $browser->get("$BASEURL/isAllowed");
-
-if ( $jobsResponse->is_success )
-{
-    my $status = parseJobQueryResponse($jobsResponse->content);
-    bail("Max jobs reached. The server cannot process your request right now; try again later.", 0) unless $status > 0;
-}
-else
-{
-    bail(sprintf("[%d] %s\n", $jobsResponse->code, parseError($jobsResponse->content)));
-}
-
-
-######
-# make a temporary input if lists were provided
-unless ( defined $INPUTFILE )
-{
-    $INPUTFILE = "$TMP/input.homemade";
-    open INPF, ">$INPUTFILE" or bail("Error writing to input file.");
-
-    if ( defined $IDLISTFILE )
-    {
-        open IDLIST, "<$IDLISTFILE" or bail("Error reading input file.");
-        while(  )
-    	{
-        	chomp;
-        	if ( /(\w{5})/ )
-        	{
-        	    print INPF ">PDBID\n$1\n";
-        	}
-        }
-        close IDLIST;
-    }
-
-
-    if ( defined $SEQFASTAFILE )
-    {
-        open FASTA, "<$SEQFASTAFILE" or bail("Error reading input file.");
-        while(  )
-    	{
-        	chomp;
-            print INPF "$_\n";
-        }
-        close FASTA;
-    }
-
-    close INPF;
-}
-
-
-######
-# prepare parameters
-print STDERR "Preparing parameters for service request...\n";
-
-my @parameters = ();
-push(@parameters, "fileinput" => ["$INPUTFILE"]);
-push(@parameters, "out_type" => $OUTTYPE);
-
-push(@parameters, "rest_flag" => "1");
-push(@parameters, "cls_flag" => "1");
-push(@parameters, "pre_flag" => "1") if defined $EVALFLAG;
-push(@parameters, "noin_flag" => "1") if defined $NOINFLAG;
-
-push(@parameters, "run_mode" => $RUNMODE);
-push(@parameters, "thread_count" => $THREADCOUNT) if $RUNMODE eq "thread";
-
-
-if ( defined $STRFLAG )
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-}
-elsif ( defined $SEQFLAG )
-{
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-else
-{
-    push(@parameters, "str_flag" => "1");
-    push(@parameters, "ash_flag" => "1");
-    push(@parameters, "seq_flag" => "1");
-    push(@parameters, "seq_algorithm" => "fast");
-    push(@parameters, "seq_database" => $SEQDATABASE);
-    push(@parameters, "seq_blastlimit" => $SEQBLASTLIMIT);
-    push(@parameters, "seq_outputlimit" => $SEQLIMIT);
-}
-
-
-
-######
-# start rest service
-print STDERR "Sending service request...\n";
-
-# post: running a mafftash job
-my $postResponse = $browser->post( $BASEURL, \@parameters, 'Content_Type' => 'form-data' );
-bail(sprintf("[%d] %s\n", $postResponse->code, parseError($postResponse->content))) unless($postResponse->is_success);
-
-
-# get response from post request
-my ($status, $seekid) = parseResponse($postResponse->content);
-
-my $MAXTRIES = 3;
-my $STIMER = 5;
-my $timer = 0;
-
-print STDERR "Request sent! Waiting for response...[$seekid]\n";
-
-my $checklist = {};
-
-# wait for results until it becomes available
-while(1)
-{
-    # sleeps for 5+random, 10+random, 15+random, 20+random, 25+random, 30+random ,,, 60+random, 60+random,,,
-    $timer = $timer >= 60 ? 60 : $timer+$STIMER;
-    sleep($timer+int(rand(4)));
-
-    # get: get results for mafftash job
-    my $getResponse = $browser->get("$BASEURL/$seekid");
-
-    if ( $getResponse->is_success )
-    {
-
-        # get response from get request
-        ($status, $seekid) = parseResponse($getResponse->content);
-        next unless ( $status eq "done" );
-
-
-        # if job is finished and ready
-        print STDERR "Results found!\n";
-        my $csfile = "$TMP/checksum";
-        my $try1 = 1;
-
-
-        while(1)
-        {
-            print STDERR "Fetching Results... [Trial $try1]\n";
-
-            if ( is_success(getstore("$BASEURL/get/$seekid/checksum", $csfile)) && -e $csfile && -s $csfile )
-            {
-                # get response from get request
-                $checklist = extractchecksum($csfile);
-                bail("Error retrieving list of compressed files!") unless ( scalar %$checklist > 0 );
-
-
-                foreach my $id ( sort keys %$checklist )
-                {
-                    sleep 1;
-                    my $checkfile = "$TMP/$id";
-                    my $checkid = $checklist->{$id};
-                    my $try2 = 1;
-
-                    while(1)
-                    {
-                        unlink $checkfile if -e $checkfile;
-
-                        if ( is_success(getstore("$BASEURL/get/$seekid/$id", $checkfile)) && -e $checkfile && -s $checkfile )
-                        {
-                            last if $ISWINDOWS;
-
-                            my $hashid = getchecksum($checkfile);
-                            #print STDERR "[hashid]$hashid [checkid]$checkid\n";
-
-                            if ($hashid ne "" && $hashid ne $checkid )
-                            {
-                                #unlink $checkfile if -e $checkfile;
-                                bail("Error retrieving compressed file from server! [Checksum Failed]") if $try2 >= $MAXTRIES;
-                                $try2++;
-                                sleep $STIMER;
-                            }
-                            else
-                            {
-                                last;
-                            }
-                        }
-                        else
-                        {
-                            bail("Error retrieving compressed file from server!") if $try2 >= $MAXTRIES;
-                            $try2++;
-                            sleep $STIMER;
-                        }
-                    }
-                }
-
-                last;
-            }
-            else
-            {
-                bail("Error retrieving list of compressed files from server!") if $try1 >= $MAXTRIES;
-                $try1++;
-                sleep $STIMER;
-            }
-        }
-
-        last;
-
-    }
-    else
-    {
-        bail(sprintf("[%d] %s\n", $getResponse->code, parseError($getResponse->content)));
-    }
-
-}
-
-
-# make sure outputs were generated
-# decompress
-print STDERR "Assembling final results...\n";
-
-foreach my $id ( sort keys %$checklist )
-{
-    if ( $id =~ /^$seekid\.out(\.str|\.seq)?/  )
-    {
-        bail("Error: Output file corrupted!") unless -e "$TMP/$id";
-        appendToFile("$TMP/$id","$OUTPUTFILE".$1);
-    }
-}
-
-cleanup();
-
-
-
-####################
-####################
-
-
-sub parseResponse
-{
-    my $response = shift;
-    my $status = "";
-    my $seekid = "";
-
-    if ( $response =~ /^([^\s:]+):([^\s:]+)$/ )
-    {
-        $seekid = $1;
-        $status = $2;
-    }
-
-    return ($status, $seekid);
-}
-
-
-sub parseJobQueryResponse
-{
-    my $response = shift;
-    my $jobs = 100;
-
-    if ( $response =~ /^(\d+)$/ )
-    {
-        $jobs = $1;
-    }
-
-    return $jobs;
-}
-
-
-sub extractchecksum
-{
-    my $infile = shift;
-    my %dataset = ();
-
-    #open CSUM, "tar -zxf $infile -O|" or return \%dataset;
-    open CSUM, "<$infile" or return \%dataset;
-
-    while()
-    {
-        chomp;
-        if ( /^(\S+)\s+(\S+)$/ )
-        {
-            $dataset{$2} = $1;
-        }
-    }
-
-    close CSUM;
-
-    return \%dataset;
-}
-
-
-sub parseError
-{
-    my $response = shift;
-
-    #"error":"Invalid number of inputs found."
-    my $errorstr = ( $response =~ /\"error\"\s*:\s*\"([^\"]+)\"/ ) ? $1 : $response;
-    return $errorstr;
-}
-
-
-sub getchecksum
-{
-    my $infile = shift;
-
-    # md5 binary check
-    my $MD5BIN = "";
-
-    if ( -x "/usr/bin/md5sum" )
-    {
-        $MD5BIN = "/usr/bin/md5sum";
-    }
-    elsif ( -x "/sbin/md5" )
-    {
-        $MD5BIN = "/sbin/md5 -q";
-    }
-
-    return "" if $MD5BIN eq "";
-
-
-    my $checksum = "";
-    open MD5EXE, "$MD5BIN $infile|" or return "";
-
-    while()
-    {
-        if (/^(\S+)\s+(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-        elsif (/^(\S+)$/)
-        {
-            $checksum = $1;
-            last;
-        }
-    }
-
-    close MD5EXE;
-
-    return $checksum;
-
-}
-
-
-sub backticks
-{
-    my $command = shift;
-
-    `$command`;
-    return ($? == -1) ? 0 : 1;
-}
-
-
-sub bail
-{
-    my $str = shift;
-    my $status = shift;
-
-    #0 for success and 1 for error
-    $status = 1 unless defined;
-
-    print STDERR "$str\n" if defined $str;
-
-    cleanup();
-
-    exit($status);
-}
-
-
-sub cleanup
-{
-    return if ($TMP eq "" || !-d $TMP);
-
-    opendir(MAINDIR, $TMP);
-    my @files = readdir(MAINDIR);
-    closedir(MAINDIR);
-
-    foreach my $file (@files)
-    {
-        unlink "$TMP/$file" if -e "$TMP/$file";
-    }
-
-    remove_tree($TMP);
-
-}
-
-
-sub appendToFile
-{
-    my $inpfile = shift;
-    my $outfile = shift;
-
-    open INPF, "<$inpfile" or bail("Server Error: Error in reading file.");
-    open OUTF, ">>$outfile" or bail("Server Error: Error in writing to file.");
-
-    while()
-    {
-        print OUTF $_;
-    }
-
-    close OUTF;
-    close INPF;
-}
-
-
-
-sub help
-{
-    my $str = shift;
-
-    print <<'HELPME';
-
-USAGE
-  ./seekquencer_premafft.pl -inp  -out  [-str|-seq]
-  ./seekquencer_premafft.pl -idf  -seqf  -out  [-str|-seq]
-
-
-PARAMETERS
-  -inp 
-     INFILE is a FASTA-formatted file
-     PDB entries are written as:
-        >PDBID
-        [5-character pdbid+chain]
-
-     While sequence entries are written as:
-        >[id]
-        [sequence]
-
-  -idf 
-     IDLISTFILE is a file containing a list of pdbids
-     pdbids should be a 5-character pdbid + chain
-
-  -seqf 
-     SEQFASTA is a fasta file
-     entries are written as:
-        >[id]
-        [sequence]
-
-  -out 
-     Results are writen to a file named OUTFILE
-
-  -str
-     Only structures will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-  -seq
-     Only sequences will be collected by Seekquencer
-     If neither -str nor -seq is set, both structures and sequences will be collected by Seekquencer
-
-
-OPTIONAL PARAMETERS:
-  -seqd 
-     Search Database for sequence homologs. Default value: uniref100
-
-  -lim 
-     this sets the maximum number of sequence homologs collected. Default value: 100
-
-  -blim 
-     this sets the -b and -v value when running blastall. Default value: 100
-
-  -pre
-     When -str is set, this will compare all structures against all using pdp-ash
-     This would ensure that all structures collected are matching
-     All structures that do not match will be removed
-
-  -noin
-     When set, inputs will not be included in the output
-
-  -mod 
-     Defines the output format
-     mafftash (default) will print a mafftash-formatted fasta file
-     mafftash-split will make 2 files separating the structures (OUTFILE.str) from sequences (OUTFILE.seq)
-     fasta will print a regular fasta file
-
-  -run 
-    thread will run simultaneous jobs during blast queries (faster but takes more nodes)
-    normal will run sequential blast queries (slower but takes less nodes)
-    Default value: normal
-
-  -trd 
-    if -run  is defined, this sets the number of parallel jobs to run. Default value: 3
-
-
-HELPME
-
-    bail($str);
-}
-
diff --git a/software/mafft/mafft-win/usr/lib/mafft/seq2regtable.exe b/software/mafft/mafft-win/usr/lib/mafft/seq2regtable.exe
deleted file mode 100755
index 3b830829..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/seq2regtable.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/setcore.exe b/software/mafft/mafft-win/usr/lib/mafft/setcore.exe
deleted file mode 100755
index 55d547df..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/setcore.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/setdirection.exe b/software/mafft/mafft-win/usr/lib/mafft/setdirection.exe
deleted file mode 100755
index 30a43ec1..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/setdirection.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/sextet5.exe b/software/mafft/mafft-win/usr/lib/mafft/sextet5.exe
deleted file mode 100755
index 9f03a81a..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/sextet5.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/splittbfast.exe b/software/mafft/mafft-win/usr/lib/mafft/splittbfast.exe
deleted file mode 100755
index 687845f5..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/splittbfast.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/tbfast.exe b/software/mafft/mafft-win/usr/lib/mafft/tbfast.exe
deleted file mode 100755
index f9ee9049..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/tbfast.exe and /dev/null differ
diff --git a/software/mafft/mafft-win/usr/lib/mafft/version.exe b/software/mafft/mafft-win/usr/lib/mafft/version.exe
deleted file mode 100755
index c1b7ee50..00000000
Binary files a/software/mafft/mafft-win/usr/lib/mafft/version.exe and /dev/null differ
diff --git a/software/versions.txt b/software/versions.txt
index 8e8ca7b8..afe86e47 100644
--- a/software/versions.txt
+++ b/software/versions.txt
@@ -1,9 +1,9 @@
 Apache-POI: 3.8
-BLAST+: 2.10.0
+BLAST+: 2.12.0
 CD-HIT: 4.8.1
-DIAMOND: 0.9.32
+DIAMOND: 2.0.13
 GLPK: 4.40
 M2HTML: 1.5
-HMMER: 3.3
-MAFFT: 7.467
+HMMER: 3.3.2
+MAFFT: 7.490
 WoLFPSORT: v0.2
diff --git a/testing/testBlast.m b/testing/testBlast.m
deleted file mode 100755
index e0c84cd9..00000000
--- a/testing/testBlast.m
+++ /dev/null
@@ -1,121 +0,0 @@
-function [success,blastStructure]=testBlast(fullCheck)
-% testBlast
-%   Performs a check for BLAST+ functionality in RAVEN. Depending on the
-%   parameter settings the user can choose between a quick check for
-%   binaries or the thorough testing while building BLAST database and
-%   running homology search with BLASTP
-%
-%   Input:
-%   fullCheck       true if the thorough BLAST+ testing should be performed
-%                   (opt, default true)
-%
-%   Output: 
-%   success         true if the test was successful, otherwise equal to
-%                   zero
-%   blastStructure	blastStructure resulting from the thorough BLAST+ check
-%
-%   NOTE: The purpose of the thorough check is to assess whether the
-%   homology search can be successfully performed using existing BLAST+
-%   binaries. This testing function is completely standalone, only
-%   requiring BLAST+ binaries and multi-FASTA file sce.fa from tutorials
-%   directory
-%
-%   Usage: [success,blastStructure]=testBlast(fullCheck)
-
-if nargin<1
-    fullCheck=true;
-end
-
-%Get the directory for RAVEN Toolbox
-[ST, I]=dbstack('-completenames');
-ravenPath=fileparts(fileparts(ST(I).file));
-
-if isunix
-    if ismac
-        binEnd='.mac';
-    else
-        binEnd='';
-    end
-elseif ispc
-    binEnd='';
-    setenv('BLASTDB_LMDB_MAP_SIZE','1000000');
-else
-    dispEM('Unknown OS, exiting.')
-    return
-end
-
-%Create an empty blastStructure. Even if a quick BLAST+ evaluation is
-%considered, blastStructure should still be in the output
-blastStructure=[];
-
-if ~fullCheck
-    fprintf(['Checking blastp' binEnd '... ']);
-    [res,~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '"']);
-    if res==1
-        fprintf('OK\n');
-    else
-        fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-    end
-    fprintf(['Checking makeblastdb' binEnd '... ']);
-    [res,~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '"']);
-    if res==1
-        fprintf('OK\n');
-    else
-        fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-    end
-else    
-    %Generate temporary names for working directory and outFile
-    tmpDB=tempname;
-    outFile=tempname;
-    
-    %Run BLAST multi-threaded to use all logical cores assigned to MATLAB
-    cores = evalc('feature(''numcores'')');
-    cores = strsplit(cores, 'MATLAB was assigned: ');
-    cores = regexp(cores{2},'^\d*','match');
-    cores = cores{1};
-    
-    %Create a temporary folder and copy multi-FASTA file there
-    [~, ~]=system(['mkdir "' tmpDB '"']);
-    copyfile(fullfile(ravenPath,'tutorial','sce.fa'),tmpDB);
-    
-    %Construct a BLAST database
-    fprintf('Testing makeblastdb... ');
-    [res, ~]=system(['"' fullfile(ravenPath,'software','blast+',['makeblastdb' binEnd]) '" -in "' fullfile(tmpDB,'sce.fa') '" -out "' tmpDB '" -dbtype prot']);
-    if res~=0
-        fprintf('Not OK\n');
-        EM=['makeblastdb did not run successfully, error: ', num2str(res)];
-        dispEM(EM,true);
-    end
-    fprintf('OK\n');
-    
-    %Run a homology search
-    fprintf('Testing blastp... ');
-    [res, ~]=system(['"' fullfile(ravenPath,'software','blast+',['blastp' binEnd]) '" -query "' fullfile(tmpDB,'sce.fa') '" -out "' outFile '" -db "' tmpDB '" -evalue 10e-5 -outfmt "10 qseqid sseqid evalue pident length bitscore ppos" -num_threads "' cores '"']);
-    if res~=0
-        fprintf('Not OK\n');
-        EM=['blastp did not run successfully, error: ', num2str(res)];
-        dispEM(EM,true);
-    end
-    fprintf('OK\n');
-    
-    %Remove temporary folder, since homology search is finished
-    [~, ~]=system(['rm "' tmpDB '" -r']);
-    
-    %Done with the BLAST, do the parsing of the text file
-    blastStructure.fromId='sce';
-    blastStructure.toId='sco';
-    A=readtable(outFile,'Delimiter',',','Format','%s%s%f%f%f%f%f');
-    blastStructure.fromGenes=A{:,1};
-    blastStructure.toGenes=A{:,2};
-    blastStructure.evalue=table2array(A(:,3));
-    blastStructure.identity=table2array(A(:,4));
-    blastStructure.aligLen=table2array(A(:,5));
-    blastStructure.bitscore=table2array(A(:,6));
-    blastStructure.ppos=table2array(A(:,7));
-    
-    %Remove the old tempfiles
-    delete([outFile '*']);
-end
-
-success=1;
-end
diff --git a/testing/testDiamond.m b/testing/testDiamond.m
deleted file mode 100755
index b7435bc6..00000000
--- a/testing/testDiamond.m
+++ /dev/null
@@ -1,113 +0,0 @@
-function [success,blastStructure]=testDiamond(fullCheck)
-% testDiamond
-%   Performs a check for DIAMOND functionality in RAVEN. Depending on the
-%   parameter settings the user can choose between a quick check for
-%   binaries or the thorough testing while building DIAMOND database and
-%   running homology search with DIAMOND
-%
-%   Input:
-%   fullCheck       true if the thorough DIAMOND testing should be
-%                   performed (opt, default true)
-%
-%   Output: 
-%   success         true if the test was successful, otherwise equal to
-%                   zero
-%   blastStructure	blastStructure resulting from the thorough BLAST+ check
-%
-%   NOTE: The purpose of the thorough check is to assess whether the
-%   homology search can be successfully performed using existing BLAST+
-%   binaries. This testing function is completely standalone, only
-%   requiring DIAMOND binary and multi-FASTA file sce.fa from tutorials
-%   directory
-%
-%   Usage: [success,blastStructure]=testDiamond(fullCheck)
-
-if nargin<1
-    fullCheck=true;
-end
-
-%Get the directory for RAVEN Toolbox
-[ST, I]=dbstack('-completenames');
-ravenPath=fileparts(fileparts(ST(I).file));
-
-if isunix
-    if ismac
-        binEnd='.mac';
-    else
-        binEnd='';
-    end
-elseif ispc
-    binEnd='';
-else
-    dispEM('Unknown OS, exiting.')
-    return
-end
-
-%Create an empty blastStructure. Even if a quick DIAMOND evaluation is
-%considered, blastStructure should still be in the output
-blastStructure=[];
-
-if ~fullCheck
-    fprintf(['Checking diamond' binEnd '... ']);
-    [res,~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '"']);
-    if res==1
-        fprintf('OK\n');
-    else
-        fprintf('Not OK! The binary must be recompiled from source before running RAVEN\n');
-    end
-else    
-    %Generate temporary names for working directory and outFile
-    tmpDB=tempname;
-    outFile=tempname;
-    
-    %Run DIAMOND multi-threaded to use all logical cores assigned to MATLAB
-    cores = evalc('feature(''numcores'')');
-    cores = strsplit(cores, 'MATLAB was assigned: ');
-    cores = regexp(cores{2},'^\d*','match');
-    cores = cores{1};
-    
-    %Create a temporary folder and copy multi-FASTA file there
-    [~, ~]=system(['mkdir "' tmpDB '"']);
-    copyfile(fullfile(ravenPath,'tutorial','sce.fa'),tmpDB);
-    
-    %Construct a DIAMOND database
-    fprintf('Testing DIAMOND makedb... ');
-    [res, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" makedb --in "' fullfile(tmpDB,'sce.fa') '" --db "' tmpDB '"']);
-    if res~=0
-        fprintf('Not OK\n');
-        EM=['DIAMOND makedb did not run successfully, error: ', num2str(res)];
-        dispEM(EM,true);
-    end
-    fprintf('OK\n');
-    
-    %Run a homology search
-    fprintf('Testing DIAMOND blastp... ');
-    [res, ~]=system(['"' fullfile(ravenPath,'software','diamond',['diamond' binEnd]) '" blastp --query "' fullfile(tmpDB,'sce.fa') '" --out "' outFile '" --db "' tmpDB '" --more-sensitive --outfmt 6 qseqid sseqid evalue pident length bitscore ppos --threads ' cores ]);
-    if res~=0
-        fprintf('Not OK\n');
-        EM=['DIAMOND blastp did not run successfully, error: ', num2str(res)];
-        dispEM(EM,true);
-    end
-    fprintf('OK\n');
-    
-    %Remove temporary folder, since homology search is finished
-    [~, ~]=system(['rm "' tmpDB '" -r']);
-    
-    %Done with the DIAMOND, do the parsing of the text file
-    blastStructure.fromId='sce';
-    blastStructure.toId='sco';
-    A=readtable(outFile,'Delimiter','\t','Format','%s%s%f%f%f%f%f');
-    blastStructure.fromGenes=A{:,1};
-    blastStructure.toGenes=A{:,2};
-    blastStructure.evalue=table2array(A(:,3));
-    blastStructure.identity=table2array(A(:,4));
-    blastStructure.aligLen=table2array(A(:,5));
-    blastStructure.bitscore=table2array(A(:,6));
-    blastStructure.ppos=table2array(A(:,7));
-    
-    %Remove the old tempfiles
-    delete([outFile '*']);
-end
-
-success=1;
-end
diff --git a/testing/unit_tests/blastPlusTests.m b/testing/unit_tests/blastPlusTests.m
new file mode 100755
index 00000000..b47c8099
--- /dev/null
+++ b/testing/unit_tests/blastPlusTests.m
@@ -0,0 +1,58 @@
+%run this test case with the command
+%results = runtests('blastPlusTests.m')
+function tests = blastPlusTests
+tests = functiontests(localfunctions);
+end
+
+function testBlastPlus(testCase)
+%This unit test comprises several functionality tests for BLAST+ in RAVEN:
+% 1. MD5 checksum check for BLAST database files. This check is applied for
+%    "phr", "pot", "psq" and "pto" files. The remaining files (i.e. "pdb",
+%    "pin" and "ptf") are not compared as these seem to be
+%    machine-specific.
+% 2. Non-parsed text check for BLAST result files. Although the content of
+%    the files is exactly the same, their MD5 hashes are somehow different
+%    between the operating systems.
+% 3. Check of resulting blastStructure against the expected one. This is
+%    done to test BLAST results parsing in RAVEN.
+
+%%
+%Get the directory for RAVEN Toolbox
+[ST, I]=dbstack('-completenames');
+ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+
+%Import structures that contain expected MD5 hashes and BLAST results
+sourceDir = fileparts(which(mfilename));
+load([sourceDir,'/test_data/expBlastResults.mat'],'expBlastStructure','expBlastReport');
+
+organismID='sce';
+fastaFile=fullfile(ravenPath,'testing','unit_tests','test_data','yeast_galactosidases.fa');
+modelIDs={'hsa' 'afv'};
+refFastaFiles={fullfile(ravenPath,'testing','unit_tests','test_data','human_galactosidases.fa') fullfile(ravenPath,'testing','unit_tests','test_data','aflavus_galactosidases.fa')};
+
+%%
+%Run BLAST
+[actBlastStructure,actBlastReport]=getBlast(organismID,fastaFile,modelIDs,refFastaFiles,true,true);
+
+%%
+%Test 1a: Check if MD5 checksums for BLAST database files are the same
+verifyEqual(testCase,actBlastReport.dbHashes,expBlastReport.dbHashes);
+
+%Test 1b: Change one of the MD5 checksums and check if test fails
+actBlastReport.dbHashes.phr{1,1}=actBlastReport.dbHashes.phr{1,2};
+verifyNotEqual(testCase,actBlastReport.dbHashes,expBlastReport.dbHashes);
+
+%Test 2a: Check if BLAST result files are the same
+verifyEqual(testCase,actBlastReport.blastTxtOutput,expBlastReport.blastTxtOutput);
+
+%Test 2b: Change actual BLAST result file and check if test fails
+actBlastReport.blastTxtOutput='empty';
+verifyNotEqual(testCase,actBlastReport.blastTxtOutput,expBlastReport.blastTxtOutput);
+
+%Test 3a: Check if BLAST structures are the same
+verifyEqual(testCase,actBlastStructure,expBlastStructure);
+
+%Test 3b: Modify actual BLAST structure and check if test fails
+actBlastStructure(1,1).toId=actBlastStructure(1,1).fromId;
+verifyNotEqual(testCase,actBlastStructure,expBlastStructure);
+end
diff --git a/testing/unit_tests/cdhitTests.m b/testing/unit_tests/cdhitTests.m
new file mode 100755
index 00000000..d3d3e82b
--- /dev/null
+++ b/testing/unit_tests/cdhitTests.m
@@ -0,0 +1,80 @@
+%run this test case with the command
+%results = runtests('cdhitTests.m')
+function tests = cdhitTests
+tests = functiontests(localfunctions);
+end
+
+function testCdhit(testCase)
+%This unit test comprises the functionality test for CD-HIT in RAVEN:
+% 1. Check for resulting file against the expected one.
+
+%%
+%Get the directory for RAVEN Toolbox
+[ST, I]=dbstack('-completenames');
+ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+
+%Identify the operating system
+if isunix
+    if ismac
+        binEnd='.mac';
+    else
+        binEnd='';
+    end
+elseif ispc
+    binEnd='.exe';
+else
+    dispEM('Unknown OS, exiting.')
+    return
+end
+
+%Import structure that contains expected MAFFT results
+sourceDir = fileparts(which(mfilename));
+load([sourceDir,'/test_data/expCdhitMafftOutput.mat'],'expCdhitMafftOutput');
+
+%Generate temporary names for working directory and outFile
+tmpDIR=tempname;
+outFile=tempname;
+
+%Run CD-HIT multi-threaded to use all logical cores assigned to MATLAB
+cores = evalc('feature(''numcores'')');
+cores = strsplit(cores, 'MATLAB was assigned: ');
+cores = regexp(cores{2},'^\d*','match');
+cores = cores{1};
+
+%Create a temporary folder and copy multi-FASTA file there
+[~, ~]=system(['mkdir "' tmpDIR '"']);
+
+sourceDir = fileparts(which(mfilename));
+copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+
+% Define WSL paths
+wslPath.fastaFile=getWSLpath([tmpDIR filesep 'yeast_galactosidases.fa']);
+wslPath.outFile=getWSLpath(outFile);
+wslPath.cdhit=getWSLpath(fullfile(ravenPath,'software','cd-hit','cd-hit'));
+
+%%
+%Run protein clustering with CD-HIT
+if ispc
+    [~, ~]=system(['wsl "' wslPath.cdhit '" -T "' num2str(cores) '" -i "' wslPath.fastaFile '" -o "' wslPath.outFile '" -c 1.0 -n 5 -M 2000']);
+else
+    [~, ~]=system(['"' fullfile(ravenPath,'software','cd-hit',['cd-hit' binEnd]) '" -T "' num2str(cores) '" -i "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" -o "' outFile '" -c 1.0 -n 5 -M 2000']);
+end
+
+%%
+%Open actual MAFFT results file
+actCdhitOutput=importdata(fullfile(outFile));
+
+%Remove the old tempfiles
+delete([outFile '*']);
+
+%Remove temporary folder, since testing is finished
+[~, ~]=system(['rm "' tmpDIR '" -r']);
+
+%%
+%Check 1a: Check if files for CD-HIT results are the same
+verifyEqual(testCase,actCdhitOutput,expCdhitMafftOutput);
+
+%Check 1b: Change actual CD-HIT results file and check if test fails
+actCdhitOutput='abc';
+verifyNotEqual(testCase,actCdhitOutput,expCdhitMafftOutput);
+end
diff --git a/testing/unit_tests/diamondTests.m b/testing/unit_tests/diamondTests.m
new file mode 100755
index 00000000..3138d89f
--- /dev/null
+++ b/testing/unit_tests/diamondTests.m
@@ -0,0 +1,57 @@
+%run this test case with the command
+%results = runtests('diamondTests.m')
+function tests = diamondTests
+tests = functiontests(localfunctions);
+end
+
+function testDiamond(testCase)
+%This unit test comprises several functionality tests for DIAMOND blastp in
+%RAVEN:
+% 1. MD5 checksum check for DIAMOND database files.
+% 2. Non-parsed text check for DIAMOND result files. Although the content
+%    of the files is exactly the same, their MD5 hashes are somehow
+%    different between the operating systems.
+% 3. Check of resulting blastStructure against the expected one. This is
+%    done to test DIAMOND blastp results parsing in RAVEN.
+
+%%
+%Get the directory for RAVEN Toolbox
+[ST, I]=dbstack('-completenames');
+ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+
+%Import structures that contain expected MD5 hashes and DIAMOND blastp
+%results
+sourceDir = fileparts(which(mfilename));
+load([sourceDir,'/test_data/expDiamondResults.mat'],'expBlastStructure','expDiamondReport');
+
+organismID='sce';
+fastaFile=fullfile(ravenPath,'testing','unit_tests','test_data','yeast_galactosidases.fa');
+modelIDs={'hsa' 'afv'};
+refFastaFiles={fullfile(ravenPath,'testing','unit_tests','test_data','human_galactosidases.fa') fullfile(ravenPath,'testing','unit_tests','test_data','aflavus_galactosidases.fa')};
+
+%%
+%Run DIAMOND blastp
+[actBlastStructure,actDiamondReport]=getDiamond(organismID,fastaFile,modelIDs,refFastaFiles,true,true);
+
+%%
+%Test 1a: Check if MD5 checksums for DIAMOND blastp database files are the same
+verifyEqual(testCase,actDiamondReport.dbHashes,expDiamondReport.dbHashes);
+
+%Test 1b: Change one of the MD5 checksums and check if test fails
+actDiamondReport.dbHashes{1,1}=actDiamondReport.dbHashes{1,2};
+verifyNotEqual(testCase,actDiamondReport.dbHashes,expDiamondReport.dbHashes);
+
+%Test 2a: Check if DIAMOND blastp result files are the same
+verifyEqual(testCase,actDiamondReport.diamondTxtOutput,expDiamondReport.diamondTxtOutput);
+
+%Test 2b: Change actual DIAMOND blastp result file and check if test fails
+actDiamondReport.diamondTxtOutput='empty';
+verifyNotEqual(testCase,actDiamondReport.diamondTxtOutput,expDiamondReport.diamondTxtOutput);
+
+%Test 3a: Check if DIAMOND blastp structures are the same
+verifyEqual(testCase,actBlastStructure,expBlastStructure);
+
+%Test 3b: Modify actual DIAMOND blastp structure and check if test fails
+actBlastStructure(1,1).toId=actBlastStructure(1,1).fromId;
+verifyNotEqual(testCase,actBlastStructure,expBlastStructure);
+end
diff --git a/testing/unit_tests/hmmerTests.m b/testing/unit_tests/hmmerTests.m
new file mode 100755
index 00000000..d17b8e8d
--- /dev/null
+++ b/testing/unit_tests/hmmerTests.m
@@ -0,0 +1,141 @@
+%run this test case with the command
+%results = runtests('hmmerTests.m')
+function tests = hmmerTests
+tests = functiontests(localfunctions);
+end
+
+function testHmmer(testCase)
+%This unit test comprises the functionality test for HMMER in RAVEN:
+% 1. Check of parsed HMMER results against the expected.
+%
+% NOTE: as hmm and HMMER results files are time-specific, no checks for
+% these files existence are done. Also, due to the way HMMER is utilized in
+% getKEGGModelForOrganism (HMMER result files can be parsed only once all
+% required hmm files are generated), the code segment involving HMMER
+% results parsing is pasted in this test function. Should the parsing problems
+% occur in the results processing, the code modifications shall be done in
+% this function and getKEGGModelForOrganism respectively.
+
+%%
+%Get the directory for RAVEN Toolbox
+[ST, I]=dbstack('-completenames');
+ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+
+%Identify the operating system
+if isunix
+    if ismac
+        binEnd='.mac';
+    else
+        binEnd='';
+    end
+elseif ispc
+    binEnd='.exe';
+else
+    dispEM('Unknown OS, exiting.')
+    return
+end
+
+%Create empty structures needed for HMMER results
+actHmmResult.genes = {};
+actHmmResult.scores = [];
+
+%Create structures that contain expected HMMER results
+expHmmResult.genes = {'sp|P41947|MEL6_YEASX','sp|P41946|MEL5_YEASX', 'sp|P41945|MEL2_YEASX', 'sp|P04824|MEL1_YEASX'};
+expHmmResult.scores = [10^-250, 10^-250, 10^-250, 10^-250];
+
+%Generate temporary names for working directory and outFile
+tmpDIR=tempname;
+outFile=tempname;
+
+%Run HMMER multi-threaded to use all logical cores assigned to MATLAB
+cores = evalc('feature(''numcores'')');
+cores = strsplit(cores, 'MATLAB was assigned: ');
+cores = regexp(cores{2},'^\d*','match');
+cores = cores{1};
+
+%Create a temporary folder and copy multi-FASTA file there
+[~, ~]=system(['mkdir "' tmpDIR '"']);
+
+sourceDir = fileparts(which(mfilename));
+copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+copyfile(fullfile(sourceDir,'test_data','human_galactosidases.fa'),tmpDIR);
+
+%%
+%Train a hidden Markov model
+[~, ~]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmbuild' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(tmpDIR,'human_galactosidases.hmm') '" "' fullfile(tmpDIR,'yeast_galactosidases.fa') '"']);
+
+%Run a homology search against the newly-trained HMM
+[~, output]=system(['"' fullfile(ravenPath,'software','hmmer',['hmmsearch' binEnd]) '" --cpu "' num2str(cores) '" "' fullfile(tmpDIR,'human_galactosidases.hmm') '" "' fullfile(tmpDIR,'yeast_galactosidases.fa') '"']);
+
+%Save the output to a file
+fid=fopen(outFile,'w');
+fwrite(fid,output);
+fclose(fid);
+
+%%
+%Parse the results
+geneCounter=0;
+fid=fopen(outFile,'r');
+beginMatches=false;
+while 1
+    %Get the next line
+    tline = fgetl(fid);
+    
+    %Abort at end of file
+    if ~ischar(tline)
+        break;
+    end
+    
+    if and(beginMatches,strcmp(tline,'  ------ inclusion threshold ------'))
+        break;
+    end
+    
+    if beginMatches==false
+        %This is how the listing of matches begins
+        if any(strfind(tline,'E-value '))
+            %Read one more line that is only padding
+            tline = fgetl(fid);
+            beginMatches=true;
+        end
+    else
+        %If matches should be read
+        if ~strcmp(tline,'   [No hits detected that satisfy reporting thresholds]') && ~isempty(tline)
+            elements=regexp(tline,' ','split');
+            elements=elements(cellfun(@any,elements));
+            
+            %Check if the match is below the treshhold
+            score=str2double(elements{1});
+            gene=elements{9};
+            if score<=10^-50
+                %If the score is exactly 0, change it to a very
+                %small value to avoid NaN
+                if score==0
+                    score=10^-250;
+                end
+                %Check if the gene is added already and, is so, get
+                %the best score for it
+                geneCounter=geneCounter+1;
+                actHmmResult.genes{geneCounter}=gene;
+                actHmmResult.scores(geneCounter)=score;
+            end
+        else
+            break;
+        end
+    end
+end
+fclose(fid);
+
+%Remove the old tempfiles
+delete([outFile '*']);
+
+%Remove temporary folder, since testing is finished
+[~, ~]=system(['rm "' tmpDIR '" -r']);
+
+%%
+%Test 1a: Check if HMMER results match the expected ones
+verifyEqual(testCase,actHmmResult,expHmmResult);
+
+%Test 1b: Modify actual HMMER results structure and check if test fails
+actHmmResult.score(2)=1;
+verifyNotEqual(testCase,actHmmResult,expHmmResult);
+end
diff --git a/testing/unit_tests/mafftTests.m b/testing/unit_tests/mafftTests.m
new file mode 100755
index 00000000..b4ffdfd4
--- /dev/null
+++ b/testing/unit_tests/mafftTests.m
@@ -0,0 +1,68 @@
+%run this test case with the command
+%results = runtests('mafftTests.m')
+function tests = mafftTests
+tests = functiontests(localfunctions);
+end
+
+function testMafft(testCase)
+%This unit test comprises the functionality test for MAFFT in RAVEN:
+% 1. Check for resulting file against the expected one.
+
+%%
+%Get the directory for RAVEN Toolbox
+[ST, I]=dbstack('-completenames');
+ravenPath=fileparts(fileparts(fileparts(ST(I).file)));
+
+%Import structure that contains expected MAFFT results
+sourceDir = fileparts(which(mfilename));
+load([sourceDir,'/test_data/expCdhitMafftOutput.mat'],'expCdhitMafftOutput');
+
+%Generate temporary names for working directory and outFile
+tmpDIR=tempname;
+outFile=tempname;
+
+%Run MAFFT multi-threaded to use all logical cores assigned to MATLAB
+cores = evalc('feature(''numcores'')');
+cores = strsplit(cores, 'MATLAB was assigned: ');
+cores = regexp(cores{2},'^\d*','match');
+cores = cores{1};
+
+%Create a temporary folder and copy multi-FASTA file there
+[~, ~]=system(['mkdir "' tmpDIR '"']);
+
+sourceDir = fileparts(which(mfilename));
+copyfile(fullfile(sourceDir,'test_data','yeast_galactosidases.fa'),tmpDIR);
+
+% Define WSL paths
+wslPath.fastaFile=getWSLpath([tmpDIR filesep 'yeast_galactosidases.fa']);
+wslPath.outFile=getWSLpath(outFile);
+wslPath.mafft=getWSLpath(fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat'));
+
+%%
+%Run protein multi-sequence alignment with MAFFT
+if ismac
+    [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-mac','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
+elseif isunix
+    [~, ~]=system(['"' fullfile(ravenPath,'software','mafft','mafft-linux64','mafft.bat') '" --auto --anysymbol --thread "' num2str(cores) '" "' fullfile(tmpDIR, 'yeast_galactosidases.fa') '" > "' outFile '"']);
+elseif ispc
+    [~, ~]=system(['wsl "' wslPath.mafft '" --auto --anysymbol --quiet --thread "' num2str(cores) '" --out "' wslPath.outFile '" "' wslPath.fastaFile '"']);
+end
+
+%%
+%Open actual MAFFT results file
+actMafftOutput=importdata(fullfile(outFile));
+
+%Remove the old tempfiles
+delete([outFile '*']);
+
+%Remove temporary folder, since testing is finished
+[~, ~]=system(['rm "' tmpDIR '" -r']);
+
+%%
+%Check 1a: Check if files for MAFFT results are the same
+verifyEqual(testCase,actMafftOutput,expCdhitMafftOutput);
+
+%Check 1b: Change actual MAFFT results file and check if test fails
+actMafftOutput='abc';
+verifyNotEqual(testCase,actMafftOutput,expCdhitMafftOutput);
+end
diff --git a/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m b/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m
new file mode 100644
index 00000000..26cb61a4
--- /dev/null
+++ b/testing/unit_tests/sortIdentifiers_and_permuteModelTests.m
@@ -0,0 +1,54 @@
+%run this test case with the command
+%results = runtests('sortIdentifiers_and_permuteModelTests.m')
+function tests = sortIdentifiers_and_permuteModelTests
+tests = functiontests(localfunctions);
+end
+
+function sortRandomizedModelTest(testCase)
+
+%Load the expected (i.e. sorted) model
+sourceDir = fileparts(which(mfilename));
+load([sourceDir,'/test_data/ecoli_textbook.mat'], 'model');
+expModel = model;
+
+%Create the actual model that will be permuted and sorted
+actModel = expModel;
+
+%Randomly permutate model, do not use RAVEN functions
+rndIdx = randperm(numel(actModel.rxns));
+fieldsToChange = {'rxns','lb','ub','rev','c','rxnNames','grRules','eccodes'};
+for i=1:numel(fieldsToChange)
+    actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+end
+actModel.S          = actModel.S(:,rndIdx);
+actModel.rxnGeneMat = actModel.rxnGeneMat(rndIdx,:);
+
+rndIdx = randperm(numel(actModel.mets));
+fieldsToChange = {'mets','metNames','metComps','metFormulas'};
+for i=1:numel(fieldsToChange)
+    actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+end
+actModel.S     = actModel.S(rndIdx,:);
+
+rndIdx = randperm(numel(actModel.genes));
+fieldsToChange = {'genes','geneShortNames'};
+for i=1:numel(fieldsToChange)
+    actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+end
+actModel.rxnGeneMat = actModel.rxnGeneMat(:,rndIdx);
+
+rndIdx = randperm(numel(actModel.comps));
+fieldsToChange = {'comps','compNames'};
+for i=1:numel(fieldsToChange)
+    actModel.(fieldsToChange{i}) = actModel.(fieldsToChange{i})(rndIdx);
+end
+[~,J]=sort(rndIdx);
+[toreplace, bywhat] = ismember(actModel.metComps,1:length(J));
+actModel.metComps(toreplace) = J(bywhat(toreplace));
+
+%Sort randomly permutated model
+actModel = sortIdentifiers(actModel);
+
+%Check that the actual model is the same as the expected model
+verifyEqual(testCase,actModel,expModel)
+end
diff --git a/testing/unit_tests/test_data/aflavus_galactosidases.fa b/testing/unit_tests/test_data/aflavus_galactosidases.fa
new file mode 100644
index 00000000..20c8730b
--- /dev/null
+++ b/testing/unit_tests/test_data/aflavus_galactosidases.fa
@@ -0,0 +1,45 @@
+>sp|B8NWY6|AGALC_ASPFN Probable alpha-galactosidase C OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=aglC PE=3 SV=2
+MFGSPKRAALAAASLLAIFGNGPSVMAQETSSNNAVVADGKTFALNGENVSYRFRVNETT
+GDLVSDHFGGSITGDLFPGFGAEALGGWVGLAGRFRREFPDHGRGDFRIPAVRIRQEAGY
+TVTDLQYQSYSVIPGKPALPGLPSTFGSEEDVTTLVVHLYDNYSSIAVDLSYSIFPKYDA
+IVRSANVTNKGTQNITVEALSSFSFDFPYEDLEMISLRGDWAREAHRQRRKVEYGLQGFG
+SSTGFSSHLHNPFLAIVHPSTTESQGEAWGFNLVYTGSFSVDVEKGSQGLTRALLGFNPS
+QLSWQLGAGETLTSPECVSVYSSDGIGGMSRSFHRLYRNHLIKSKFATSDRPPLLNSWEG
+LYFDYNESTIYRLAEESAALGVKLFVMDDGWFGDKYPRVSDNAGLGDWVPNPDRFPDGLT
+PLVEDVTKLKAGNSSTDLRFGLWVEPEMANPNSTLYHEHPDWVLHAGQYPRTLQRNQLVL
+NLALPEVQDYIIDEITNILNSSAISYVKWDFNRAMHETPSPSNDHEYILGMYRVFDTLTT
+RFPDVLWEGCASGGGRFDPGVLEYFPQIWTSDNTDALMRITIQLGTSLAYPPSAMGAHLS
+AVPNAQTGRTIPVKFRGHVAMMGGSFGLELDPAELQEDEKAEVPGLIALAEKVNPIILTG
+DMWRLRLPEESNWPAVLFISEDGNQAVLFYFQLGPNVNHATPWLRLQGLDPKATYSVDGN
+GSYSGATLMNMGLQYKFESDYDSKVVFLQKQ
+>sp|B8MWJ5|AGALA_ASPFN Probable alpha-galactosidase A OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=aglA PE=3 SV=1
+MRLITRWIPLANALASTMPVQVVASIENPSLLPTPPMGFNNWARFMCDLNETLFVETTDA
+MASNGLLEAGYNRINLDDCWMNYDRAENGSLEWNVTKFPRGLPWLGQYVKSKGFNFGIYE
+DSGNLTCGGYPGSEGYEEIDAETFAAWGIDYLKLDGCNVYPKEGRTLQEEYKYLYGNWHE
+ILSKMQQPLIFSESAPAYFSMTDNLTDWHTVMDWVPEYGELARHSVDILVYSGEGSAWDS
+IMTNYKFNTLVARYQRPGYYNDPDFLIADHPGLSLDEKRSQFALWASFSAPLIISAHIPD
+LSSEDLEYLTNQALIAVDQDPLAQQATLASRDGSLDVLTRNLADGSRLVTILNHGSESIE
+TDISLDILGLSTDCTYKAQDLWGGSTQTIKDAIRIKLNTHATAVYKIDTDEKCSQVIPTG
+LIFNTASGKCLTGTSSSVGSESCNGSKSQIWQIDASGVIRTLSEQSKCLTADGKAISLQE
+CSENNGQKWSYAITGNLKNADTGYCLTNGGGVSACGFETNSQVFGLPAGVHVAL
+>sp|B8N7Z0|AGALD_ASPFN Probable alpha-galactosidase D OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=aglD PE=3 SV=1
+MLPKIFYLSLLPAALGHPHLQPRLDNGLARTPQMGWNTYNHYSCSPNETIVRSNAQALVD
+LGLASLGYRYVTTDCGWTVADRLSDGSLTWNETLFPEGFPALGKYLHDLDLLFGVYQDSG
+IKLCGSPPDNVGNYEDQDARTFASWEVDSLKYDNCYSDAATGYPNVNYEPSTSPQPRFAN
+MSRALAAQNRSMVFQVCEWGIDFPARWAPALGHSWRIGNDIIPHWRAIYRTLNQAVPQTS
+FAGPGQWPDLDMLFVGNDILSIPEEQTHFSLWAILKSPLTIGAALKDDETSINDESLQIL
+KQADIIGYNQDSLGVSASLRRRWTEEGYEVWSGPLSGGRTVAALINWRNESRDLTLDLPD
+IGLQYAGTVKNIWDGTTAQNVKTSYTAKVQGHGTILLELQDTTASGQYPGDTFATSTGSS
+TTFESIYGVTTSFRYNITVKLSEASSSSDVKIQSTASNKTITAQVSASGTEASAQIPLLA
+GSSNSITIVSPQSVDAITITPPNGTYFPNTAFTTIGDADTVSCGAGYCQPVGSKIGNIST
+NGTARAVIPATAGTKYLAIDYINNDVAFDSAWDWGSNSRNLTVSVNGNKPVRIEVPLSGQ
+HSELFGPGKGWWDTATIGVLTEGWKDGDNDVVIGNEGGESGFTSYGPDFVGLRVL
+>sp|B8N306|AGALB_ASPFN Probable alpha-galactosidase B OS=Aspergillus flavus (strain ATCC 200026 / FGSC A1120 / NRRL 3357 / JCM 12722 / SRRC 167) OX=332952 GN=aglB PE=3 SV=1
+MQRYISLSVSLSLLSGANALVRPDGVGRLPALGWNTWNAFGCDIDASKVLTAAEETINLG
+LKDAGYEYINIDDCWSVKSGRDPNTKRIIPDSAKFPDGISGVASKIHDLGLKVGIYSSAG
+TETCAGYPASLGYEKIDAESFAEWGIDYLKYDNCGVPTNWTDTYTHCVPDNSNGSKFPNG
+TCPDISNPAPTAYDWSSSNTAQRYNAMRDALLGVNRTILYSLCEWGQADVNTWGNGTGNS
+WRTTGDITPDWSRIVEIANENSFLMNYADFWGYPDPDMLEVGNGNLTLEENRAHFALWAA
+MKSPLIIGTALDSINEEHLAILKNKPLLSFHQDPVIGRPAYPYKWGYNPDWTFDPAHPAE
+YWSGPSSTLGGTLVLMFNSEDSAKHRTAVWSEIPELKDSAEKGSGYRVTDIWTGEDLGCV
+KDQYDVELQSHDIAALVVGESC
diff --git a/testing/unit_tests/test_data/ecoli_textbook.mat b/testing/unit_tests/test_data/ecoli_textbook.mat
new file mode 100644
index 00000000..546abbae
Binary files /dev/null and b/testing/unit_tests/test_data/ecoli_textbook.mat differ
diff --git a/testing/unit_tests/test_data/expBlastResults.mat b/testing/unit_tests/test_data/expBlastResults.mat
new file mode 100644
index 00000000..051bfa72
Binary files /dev/null and b/testing/unit_tests/test_data/expBlastResults.mat differ
diff --git a/testing/unit_tests/test_data/expCdhitMafftOutput.mat b/testing/unit_tests/test_data/expCdhitMafftOutput.mat
new file mode 100644
index 00000000..6d80662d
Binary files /dev/null and b/testing/unit_tests/test_data/expCdhitMafftOutput.mat differ
diff --git a/testing/unit_tests/test_data/expDiamondResults.mat b/testing/unit_tests/test_data/expDiamondResults.mat
new file mode 100644
index 00000000..d064d42c
Binary files /dev/null and b/testing/unit_tests/test_data/expDiamondResults.mat differ
diff --git a/testing/unit_tests/test_data/human_galactosidases.fa b/testing/unit_tests/test_data/human_galactosidases.fa
new file mode 100644
index 00000000..13b2b0a0
--- /dev/null
+++ b/testing/unit_tests/test_data/human_galactosidases.fa
@@ -0,0 +1,39 @@
+>sp|P07602|SAP_HUMAN Prosaposin OS=Homo sapiens OX=9606 GN=PSAP PE=1 SV=2
+MYALFLLASLLGAALAGPVLGLKECTRGSAVWCQNVKTASDCGAVKHCLQTVWNKPTVKS
+LPCDICKDVVTAAGDMLKDNATEEEILVYLEKTCDWLPKPNMSASCKEIVDSYLPVILDI
+IKGEMSRPGEVCSALNLCESLQKHLAELNHQKQLESNKIPELDMTEVVAPFMANIPLLLY
+PQDGPRSKPQPKDNGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADI
+CKNYISQYSEIAIQMMMHMQPKEICALVGFCDEVKEMPMQTLVPAKVASKNVIPALELVE
+PIKKHEVPAKSDVYCEVCEFLVKEVTKLIDNNKTEKEILDAFDKMCSKLPKSLSEECQEV
+VDTYGSSILSILLEEVSPELVCSMLHLCSGTRLPALTVHVTQPKDGGFCEVCKKLVGYLD
+RNLEKNSTKQEILAALEKGCSFLPDPYQKQCDQFVAEYEPVLIEILVEVMDPSFVCLKIG
+ACPSAHKPLLGTEKCIWGPSYWCQNTETAAQCNAVEHCKRHVWN
+>sp|P17050|NAGAB_HUMAN Alpha-N-acetylgalactosaminidase OS=Homo sapiens OX=9606 GN=NAGA PE=1 SV=2
+MLLKTVLLLGHVAQVLMLDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMAD
+RMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYA
+DMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATG
+RPIAFSCSWPAYEGGLPPRVNYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQ
+PVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNP
+LMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNF
+TGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQ
+>sp|Q06187|BTK_HUMAN Tyrosine-protein kinase BTK OS=Homo sapiens OX=9606 GN=BTK PE=1 SV=3
+MAAVILESIFLKRSQQKKKTSPLNFKKRLFLLTVHKLSYYEYDFERGRRGSKKGSIDVEK
+ITCVETVVPEKNPPPERQIPRRGEESSEMEQISIIERFPYPFQVVYDEGPLYVFSPTEEL
+RKRWIHQLKNVIRYNSDLVQKYHPCFWIDGQYLCCSQTAKNAMGCQILENRNGSLKPGSS
+HRKTKKPLPPTPEEDQILKKPLPPEPAAAPVSTSELKKVVALYDYMPMNANDLQLRKGDE
+YFILEESNLPWWRARDKNGQEGYIPSNYVTEAEDSIEMYEWYSKHMTRSQAEQLLKQEGK
+EGGFIVRDSSKAGKYTVSVFAKSTGDPQGVIRHYVVCSTPQSQYYLAEKHLFSTIPELIN
+YHQHNSAGLISRLKYPVSQQNKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGK
+WRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANG
+CLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDF
+GLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYER
+FTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
+>sp|P06280|AGAL_HUMAN Alpha-galactosidase A OS=Homo sapiens OX=9606 GN=GLA PE=1 SV=1
+MQLRNPELHLGCALALRFLALVSWDIPGARALDNGLARTPTMGWLHWERFMCNLDCQEEP
+DSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQL
+ANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENL
+ADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIK
+SILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDL
+RHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIG
+GPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENT
+MQMSLKDLL
diff --git a/testing/unit_tests/test_data/yeast_galactosidases.fa b/testing/unit_tests/test_data/yeast_galactosidases.fa
new file mode 100644
index 00000000..894ec4d0
--- /dev/null
+++ b/testing/unit_tests/test_data/yeast_galactosidases.fa
@@ -0,0 +1,36 @@
+>sp|P04824|MEL1_YEASX Alpha-galactosidase 1 OS=Saccharomyces cerevisiae OX=4932 GN=MEL1 PE=1 SV=1
+MFAFYFLTACISLKGVFGVSPSYNGLGLTPQMGWDNWNTFACDVSEQLLLDTADRISDLG
+LKDMGYKYIILDDCWSSGRDSDGFLVADEQKFPNGMGHVADHLHNNSFLFGMYSSAGEYT
+CAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPEISYHRYKAMSDALNKTGRP
+IFYSLCNWGQDLTFYWGSGIANSWRMSGDVTAEFTRPDSRCPCDGDEYDCKYAGFHCSIM
+NILNKAAPMGQNAGVGGWNDLDNLEVGVGNLTDDEEKAHFSMWAMVKSPLIIGANVNNLK
+ASSYSIYSQASVIAINQDSNGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALL
+NGGSVSRPMNTTLEEIFFDSNLGSKKLTSTWDIYDLWANRVDNSTASAILGRNKTATGIL
+YNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPSS
+>sp|P41947|MEL6_YEASX Alpha-galactosidase 6 OS=Saccharomyces cerevisiae OX=4932 GN=MEL6 PE=3 SV=1
+MFAFYFLTACISLKGVFGVSPSYNGLGLTPQMGWDNWNTFACDVSEQLLLDTADRISDLG
+LKDMGYKYVILDDCWSSGRDSDGFLVADKHKFPNGMGHVADHLHNNSFLFGMYSSAGEYT
+CAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPDVSYHRYKAMSDALNKTGRP
+IFYSLCNWGQDLTFYWGSGIANSWRMSGDITAEFTRPDSRCPCDGDEYDCKYAGFHCSIM
+NILNKAAPMGQNAGVGGWNDLDNLEVGVGNLTDDEEKAHFSMWAMVKSPLIIGADVNHLK
+ASSYSIYSQASVIAINQDPKGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALL
+NGGSVARPMNTTLEEIFFDSNLGSKELTSTWDIYDLWANRVDNSTASAILEQNKAATGIL
+YNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPSA
+>sp|P41945|MEL2_YEASX Alpha-galactosidase 2 OS=Saccharomyces cerevisiae OX=4932 GN=MEL2 PE=3 SV=1
+MFAFYFLTACISLKGVFGVSPSYNGLGLTPQMGWDNWNTFACDVSEQLLLDTADRISDLG
+LKDMGYKYIILDDCWSSGRDSDGFLVADEQKFPNGMGHVADHLHNNSFLFGMYSSAGEYT
+CAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPEISYHRYKAMSDALNKTGRP
+IFYSLCNWGQDLTFYWGSGIANSWRMSGDITAEFTRPDSRCPCDGDEYDCKYAGFHCSIM
+NILNKAAPMGQNAGVGGWNDLDNLEVRVGNLTDDEEKAHFPMWAMVKSPLIIGADVNTLK
+PSSYSIYSQASVIAINQDPKGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALL
+NGGSVPRPMNTTLEEIFFDSNLGSKELTSTWDIYDLWANRVDNSTASAILGQNKTATGIL
+YNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPSA
+>sp|P41946|MEL5_YEASX Alpha-galactosidase 5 OS=Saccharomyces cerevisiae OX=4932 GN=MEL5 PE=3 SV=1
+MFAFYFLTACTTLKGVFGVSPSYNGLGLTPQMGWDSWNTFACDVSEQLLLDTADRISDLG
+LKDMGYKYVILDDCWSSGRDSDGFLVADKHKFPNGMGHVADHLHNNSFLFGMYSSAGEYT
+CAGYPGSLGREEEDAQFFANNRVDYLKYDNCYNKGQFGTPDVSYHRYKAMSDALNKTGRP
+IFYSLCNWGQDLTFYWGSGIANSWRMSGDITAEFTRPDSRCPCDGDEYDCKYAGFHCSIM
+NILNKAAPMGQNAGVGGWNDLDNLEVGVGNLTDDEEKAHFSMWAMVKSPLIIGADVNHLK
+ASSYSIYSQASVIAINQDPKGIPATRVWRYYVSDTDEYGQGEIQMWSGPLDNGDQVVALL
+NGGSVARPMNTTLEEIFFDSNLGSKELTSTWDIYDLWANRVDNSTASAILEQNKAATGIL
+YNATEQSYKDGLSKNDTRLFGQKIGSLSPNAILNTTVPAHGIAFYRLRPSA
diff --git a/testing/unit_tests/tinitTests.m b/testing/unit_tests/tinitTests.m
old mode 100644
new mode 100755
diff --git a/tutorial/tutorial5.m b/tutorial/tutorial5.m
index e47bcd78..f408339b 100755
--- a/tutorial/tutorial5.m
+++ b/tutorial/tutorial5.m
@@ -19,10 +19,10 @@
 %are for. This process takes up to 20-35 minutes in macOS, Unix systems and
 %40-55 minutes in Windows, depending on your hardware and the size of
 %target organism proteome
-model=getKEGGModelForOrganism('sce','sce.fa','euk100_kegg94','output',false,false,false,false,10^-30,0.8,0.3,-1);
+model=getKEGGModelForOrganism('sce','sce.fa','euk90_kegg100','output',false,false,false,false,10^-30,0.8,0.3,-1);
 
-%The resulting model should contain around 1669 reactions, 1677
-%metabolites and 838 genes. Small variations are possible since it is an
+%The resulting model should contain around 1590 reactions, 1571
+%metabolites and 837 genes. Small variations are possible since it is an
 %heuristic algorithm and different KEGG versions will give slightly
 %different results.
 disp(model);