How to annotate orthogroups?

[Ruiqi-CUB]

Hi David!

I am using OrthoFinder output for CAFE and I would like to know the functions of the orthogroups that are expanded or extracted.

I annotated each genomes used for OrthoFinder with eggnog mapper.

I am not sure how to annotate the orthogroup though: each orthogroup has serveral genes from different species, and their annotation is always not the same. How can I annotate each orthogroup? Should I get the function (for example, gene name) of each gene in that orthogroup, calculate the frequency, then pick the most frequent function?

Thanks Ruiqi