Merge pull request #47 from andrewjpage/cleanup_intermediate_files

Cleanup intermediate files

ChangeLog

@@ -1,2 +1,7 @@
+2012-8-7 Andrew J. Page <[email protected]>
+* Cleanup intermediate files by default
+* Fix RF distance calculation and comparison
+
 2012-4-24 Andrew J. Page <[email protected]>
 * Initial beta testing version
+

INSTALL

@@ -4,11 +4,16 @@ make install
 
 The main executable should be in ./src/gubbins
 
-
-These applications must be in your PATH:
-FastTree http://www.microbesonline.org/fasttree/
-RAxML (the full version) http://sco.h-its.org/exelixis/software.html
+These applications must be already installed in your PATH:
+FastTree (>=2.1.4) http://www.microbesonline.org/fasttree/
+RAxML (>=7.2.8, the full version) http://sco.h-its.org/exelixis/software.html
+Python 2.7
 
 These Python packages must be in your PYTHONPATH:
-Biopython (>=1.59)
+Biopython 	(>=1.59)
 DendroPy (>=3.11.1)
+ReportLab (>= 2.5)
+
+
+To run the application:
+run_gubbbins.py my_alignment.aln

README

@@ -1,25 +1,7 @@
-This application takes in a multi fasta alignment, finds all the SNP sites, then outputs the snp sites in the following formats:
-VCF, 
-a multi fasta alignment,
-relaxed phylib format.
+This application takes in a multi fasta alignment and detects recombination regions.
 
-The first sequence in the input file is taken as the reference.
+To use it:
+run_gubbins.py my_alignment.aln
 
-To use:
-
-multi_fasta_to_vcf my_file.aln
-
-
-VCF
-=====
-This contains the position of each SNP in the reference sequence, and the occurance in each other sample.
-
-Multi Fasta Alignment
-=====
-Similar to the input file but just containing the snpsites.
-
-Relaxed Phylib format
-=====
-All the snpsites in a format for RAxML
 
 

VERSION

@@ -0,0 +1 @@
+0.1