Ortholuge 0.8 README --------------------- OVERVIEW Ortholuge is a high-througput pipeline that can generate precise ortholog predictions between two species on a genome-wide scale. The program analyzes the phylogenetic distances for genes or proteins from 2 ingroup species (species being compared) relative to genes from an outgroup species, and identifies which genes are most likely to be ssd-orthologs ("Supporting Species Divergence" orthologs) and may most likely have the same function. It also identifies probable paralogs in a list of putative orthologs. Users can either supply their own list of putative ortholog "triples" (putative orthologs from the 2 ingroups and 1 outgroup) for analysis or they can supply three FASTA files of gene or protein sequences from the species' genomes, so that the putative orthologs can be initially determined based on a reciprocal-best-blast analysis. Ortholuge then aligns the sequences using MUSCLE, edits the alignments using previously determined criteria, calculates phylogenetic distance ratios using PHYLIP (with EMBOSS), and plots phylogenetic distance ratios in user-friendly graphical outputs. The resulting Ortholuge ratios and graphs can be flexibly used to identify orthologs most likely to have the same function and eliminate probable paralogs from a dataset of orthologs. Note that this process is not meant to be interactive, it's a high through-put pipeline suitable for genome-scale analysis, hence there is no user interface. For more information, see http://www.pathogenomics.ca/ortholuge ----------------------------------------------------------------------------- INSTALLATION To install this package, please refer to the INSTALL file included with the distribution. ----------------------------------------------------------------------------- QUESTIONS? PROBLEMS? COMMENTS? Email ortholuge-mail@sfu.ca (contact person: Matthew Laird) and we'd be happy to help. ----------------------------------------------------------------------------- BUG REPORTING If you find a bug, please report it to ortholuge-mail@sfu.ca along with the following information: * version of Perl (output of 'perl -V' is best) * version of Ortholuge * operating system type and version * exact text of error message or description of problem * config file or arguments being used If we don't have access to a system similar to yours, you may be asked to insert some debugging lines and report back on the results. The more help and information you can provide, the better! ----------------------------------------------------------------------------- COPYRIGHT AND LICENCE Ortholuge and it's associated modules are Copyright (C) 2005 Matthew Laird and Fiona Brinkman. All rights reserved. This program is distributed under the GNU General Public License. See also the LICENSE file included with this package. ----------------------------------------------------------------------------- AUTHOR INFORMATION An Ortholuge prototype was originally written by Benjamin Horsman and Fiona Brinkman and improved upon by Debra Fulton and Yvonne Li. The Ortholuge distribution package was written by Matthew Laird of the Brinkman Laboratory at Simon Fraser University, Burnaby, BC, Canada http://www.pathogenomics.sfu.ca/brinkman ----------------------------------------------------------------------------- ACKNOWLEDGEMENTS Thanks to all of the members of the SFU Brinkman Laboratory for being particularly helpful during the development process of this package.