[Inparanoid] low number of orthologs

[Arjun Subedi]

Dear inparanoid developers,

I am using inparanoid to derive orthologs for a newly sequenced fungus. My
organism consists 12000 protein sequence. When I run the inparanoid with
default settings against yeast (as protein B) it yields only 60 orthologs,
which I think is a very low number. Then I splitted the sequence of both
organism and took only half of the sequences of each organism. Then I run a
inparanoid, and it gives higher no of othologs (214). Does it mean
something wrong in my sequence file or any other issues with bigger file?

Thank you

Arjun Subedi
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