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

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?

genome ortholog
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updated by Ram Ram • written by 123abcmathematics • 123abcmathematics

2 answers

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.

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written by h.mon h.mon

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

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

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written by Adrian Pelin Adrian Pelin

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