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!

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.



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.
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News

Summer/Fall 2010
By: admin on 02-21-2011 at 10:52
Lots of things have changed! Phylomarke... Read More
Spring/Summer 2010
By: admin on 06-15-2010 at 02:06
Website has been updated to a new style.... Read More
Summer/Fall 2009
By: admin on 06-15-2010 at 02:03
run.pl has been extensively developed. P... Read More
Spring 2009
By: admin on 06-15-2010 at 02:01
Source code has been tested quite extens... Read More
2008
By: admin on 06-15-2010 at 02:01
Thaine Rowley took over the project. ... Read More
Enjoy!