I have the results from codeml analysis where I have identified few sites that are under positive selection in my target species. I am now looking for the change in amino acid in the nearest species and the ancestral amino acid. I have around 20 such genes where I have identified positive selection in orthologs of these genes. I can easily identify the amino acid in nearest species from the MSA of these genes. I am wondering if it is fair enough to identify the ancestral amino acid same way- looking at MSA for amino acid in the distant species retained in the orthology cluster. or there is any other way to construct the ancestral state of these sites?
I hope I am clear in asking the question.