I've run OrthoFinder with a list of 15 animal proteomes and I got the inferred orthogroups and the relative trees. The results look good but I would like to obtain further information regarding the relationships between the orthogroups. So I thought to cluster the orthogroups between them and produce a bigger tree with, as leaves, the inferred orthogroups. I tried using Clustal Omega on the sequences from a group of orthogroups of interest, but some of the relationships inferred by OrthoFinder were lost. Any suggestions on how I can do this?
Thank you in advance for you time and consideration.