Could you, please, help me? I was running Orthomcl-program, using a small bacterial taxon. I used their *.faa versions for each genome, just proteins.
I was going to find bona fide orthologs only, but occasionally I realized that as a result I have a mixture of bona fide orthologs, co-orthologs and in-paralogs! Is GETHOGs my only way to find bona fide orthologs, or there are some other procedures to get rid of these co-orthologs and in-paralogs in the Orthomcl output? I thought, the "named groups" from Orthomcl is a solution I was looking for, but unfortunately I was wrong.
Thank you very much!