Given 3 FASTA files, how can I find putative orthologs?

Question

[123abcmathematics]

I have the CDS FASTA files for 3 organisms. I was wondering if there was a quick script, set of online tools, or methods to find the 3-way orthologs between these 3 organisms using the CDS FASTA files?

Answer 1

[h.mon]

There are loads of options. For example, OMA and OrthoMCL are two popular software. You can look at MCL page under protocols for a quick how-to on clustering blast results - probably the simplest solution for you. You could also read old posts for suggestions, e.g. here and here.

[Christophe Dessimoz]

To use OMA on your own fasta files, use the standalone version here: http://omabrowser.org/standalone

Answer 2

[Adrian Pelin]

For just 3, I would use inparanoid, it does pairwise comparisons:

http://software.sbc.su.se/cgi-bin/request.cgi?project=inparanoid