I used the branch-site method to detect positive selection in a linea with codeml. Now I would like to be sure that the positive selection I detected is really positive selection and not a consequence of BGC. For that, I need to know which substitutions occured in my significative sites. As I have the position of the sites, I just need to know which sequence is used as the ancestral sequence and from that I will deduce what was the substitution.
How can I find which sequence is used as the ancestral sequence?
Thank you a lot,