Ortholuge 0.8 README
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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

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INSTALLATION

To install this package, please refer to the INSTALL file included with
the distribution.

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QUESTIONS? PROBLEMS? COMMENTS?

Email ortholuge-mail@sfu.ca (contact person: Matthew Laird) and we'd be happy to help.

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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!

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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.

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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

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ACKNOWLEDGEMENTS

Thanks to all of the members of the SFU Brinkman Laboratory for being
particularly helpful during the development process of this package.
