I have a situation where I am trying to find orthologs among a collection of metazoan proteomes. I've decided to use OrthoFinder for this purpose. The OrthoFinder documentation claims "The accuracy can be increased still further (20% more accurate on Orthobench) by including outgroup species," (towards the end of the first paragraph here), and therefore I'd like to include an outgroup in the analysis.
Now my question is: what would be a good choice for an outgroup here? I was thinking of something not too distant (like a well-studied fungus, for example).
I am also not entirely sure about including an outgroup to begin with. The OrthoFinder documentation is (to me) confusing, and seems to be sending across mixed signals. For instance, here (first paragraph after the first set of bullet points), the documentation suggests not including an outgroup. So I'm not entirely sure what to do. (Phylogenetics and company are not my forte.)
Can anybody advise me on this? Inputs from those who have used OrthoFinder in similar contexts would be much appreciated. (Others are naturally welcome also!!)
