Phylomarker

This is version 3.0. This contains many improvements including: everything controlled from one file (run.pl), seperate coverage and identity flags for single copy exon comparison and ortholog comparison, and the ability to use more than 2 genomic datafiles.
This version also includes Intron marker search and Exon/Intron marker search!

PhyloMarker 3.0
Read Me

This is version 2.0. This contains many improvements including: everything controlled from one file (run.pl), seperate coverage and identity flags for single copy exon comparison and ortholog comparison, and the ability to use more than 2 genomic datafiles.

PhyloMarker 2.0
Read Me

This is version 1.0 and is OLD. It is kept here in case people decide they still want to use this code. 2.0 is above and contains many improvements over this version.

1. extract_genbank_ exons.pl: parses the GenBank files, and extract exons that meet the criteria of having a length greater than what you set up.
2. blast_parser.pl: finds putative single copy exons from a self genome BLAST comparison.
3. ortholog_parser.pl: finds putative orthologs from a cross genome BLAST comparison.

This README file describes in detail how to run the scripts and includes a step-by-step tutorial for the bioinformatics pipeline.

These programs are dual-licensed under the GPLv3 and Commercial Licenses. Basically, it's open source, if you dont want to share the source code, you need to buy a commercial license to distribute.