Are othrogroups created by OrthoFinder mutually exclusive and exhaustive? How are isoforms of a gene handled?

[soumitrakp]

Dear Developer,

Thank you for creating such a useful tool that benefits many in the research community. I have a three questions regarding the orthogroups generated by OrthoFinder:

1. Are the orthogroups mutually exclusive? In other words, can a gene G from species S be present in two different orthogroups (e.g., OG1 and OG2)?

2. Are the orthogroups exhaustive? In other words, must every gene G from species S be present in at least one orthogroup (OG)?

3. If the input contains multiple proteins (isoforms) for a single gene, how does OrthoFinder handle them? Specifically, does OrthoFinder group all isoforms of a gene into the same orthogroup?

Please let me know if any clarification is needed.

Best regards,
Soumitra

[lauriebelch]

Hi Soumitra,

1. Orthogroups are mutually exclusive, a gene can only be in one orthogroup
2. Some genes are unassigned, so don't end up in any orthogroup
3. We reccomend that you only use one transcript per gene (there is a script that can do this for you). If you run multiple isoforms, they will probably end up in the same orthogroup, but orthofinder will take much longer to run

Hope this is helpful!

[soumitrakp]

Thank you, @lauriebelch, for your helpful comments! Could you please share a link to the script mentioned in question 3?