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Can Orthofinder produce FastA?

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

orthofinder cazy sequence alignment
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written by bsp017 • bsp017

Would the following option be relevant in your case?

os               Stop after writing sequence files for orthogroups
                   (requires '-M msa')
• 1 views • link
written by Sej Modha Sej Modha

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.

• 1 views • link
written by bsp017 • bsp017

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