synonymous substitution rates from OrthoFinder orthogroups

[MatthewHaasUMN]

Hi all,

I am trying to calculate synonymous substitution rates using orthogroups from OrthoFinder. I'm able to filter the orthogroups using regular expressions in Python, but I am still left with more genes from my species of interest (and related species to make the comparison). I am not sure how best to decide which ortholog is the ancestor and which is the descendent.

I thought of using BLAST, but my understanding is that OrthoFinder already uses BLASTP to make the assignment of genes to orthogroups.

I am doing alignment with Clustal Omega, backtranslation with a custom script, and synonymous substitution rates with PAML.

Thanks in advance.
Matthew