This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Orthomcl Pairs

hi all, i am getting a populated InParalog table but empty ortholog and coortholog tables, i have set the % match to 20% but still the tables are empty.Any ideas?

• 2,928 views • link
updated by Torst Torst • written by jollymrt • jollymrt

Can you give more detail of what you are doing using what technologies/software and what exactly goes wrong?

• 0 views • link
written by Niek De Klein Niek De Klein

I am using orthoMCL 2.0.3 to identify orthologs for a small set of proteins.the problem is I am getting populated InParalog table but nothing goes in the ortholog table.

• 0 views • link
written by jollymrt • jollymrt

1 answer

OrthoMCL will only find orthologs if you give it separate files for each organism. If you put them all in one file it thinks they are all from the same organism, and hence calls them paralogs instead.

eg. orthomcl.pl --mode 1 --fa_files Species1.faa,Species2.faa

• 1 views • link
written by Torst Torst

Log in to answer this question.

More posts like this