Can Orthofinder produce FastA?

Question

[bsp017]

Is it possible to get a FastA file of orthologs using Orthofinder? I ran orthofinder (v2.2.7) like this:

orthofinder.py -f sane_files/ -t 40 -M msa

I got around 9000 orthogroups from my genomes. I would like to Blast these against some databases e.g. CAZy database. But I need a FastA file.

Thanks,

James

[Sej Modha]

Would the following option be relevant in your case?

os               Stop after writing sequence files for orthogroups
                   (requires '-M msa')

[bsp017]

Adding that command gives the proteins that make up the orthogroup. I was wanting a single consensus sequence for each orthogroup. Not sure if there is an easy way to do that? For example, I got 9000 orthogroups, so I wanted a FastA file with 9000 proteins.