get_homologues-est
This release ships with several changes and fixes:
03032020: improved regex at sub read_cluster_config (lib/HPCluster.pm)
10032020: fixed annotate_cluster.pl -D in cases with no Pfam hits
10032020: updated regex to detect peptide sequences in lib/phyTools.pm
08042020: updated mview version to 1.67 which now shows masked sequences with Xs and not gaps
08042020: updated annotate_cluster.pl to use mview 1.67
09042020: added make clean to mcl compilation in install.pl
10042020: v2.4_10Apr20, added option -b for par(mar()) and improved options documentation to hcluster_pangenome_matrix.sh
20042020: updated hcluster_pangenome_matrix.sh to v2.4_10Apr20 to eliminate warning message
20042020: acknowledged possible bug in section 4 of plot_matrix_heatmap.sh
20042020: added arg $testR to hcluster_pangenome_matrix.sh and plot_matrix_heatmap.sh tests to check R packages
20042020: updated test_get_homologues.t, Makefile & .travis.yml
20042020: updated ubuntu to bionic (18.04) in travis.yml to match docker OS
20042020: added libgd-dev to travis.yml
21042020: added check to get_homologuespl when printing aligned coords
21042020: fixed index seek for EST jobs in check_BDBHs.pl
27042020: updated annotate_cluster.pl to scape forbidden chars in sequence names that trouble mview
29042020: updated install instructions for R modules imported by hcluster_pangenome_matrix.sh
02062020: added -n dryrun to get_homologues.pl
09072020: install.pl now tries curl before wget in macOS
31072020: downgraded cluster_pangenome_matrix.sh plot_matrix_heatmap.sh to simplify R deps
25082020: improved warning for gbk files with no nucleotide seqs in get_homologues.pl
08092020: fixed indentation of R code within compare_clusters.pl
30102020: fixed -m dryrun
10112020: replaced ' with - in $cluster_name in get_homologuespl
10112020: compare_clusters.pl stops if intersection==0
10112020: updated if else Venn R code in compare_clusters.pl
16112020: added real test of transcripts2cdsCPP.pl, not used for travis
17112020: fixed bug and improved documentation of pfam_enrich.pl
17022021: added -m dryrun to get_homologues-est.pl
17022021: fixed _cluster_makeIsoform.pl
17022021: updated bin/mcl-14-137 and made mview executable
17022021: added get_homologues-est.pl -m dryrun to test and manuals