I have 4 gene trees and would like to test for positive selection in species for each tree. I've read some of the manual, but am still confused by what to do. I want to look at the branches as well as the sites so would I use the Branch Site Model or the Clade Models (C and D)? If so, how would I do it without using command line?
I ran my aligned sequences and unrooted gene tree through CodeML in PAML with the default parameters, but I'm not sure what to do with the output files or if they are even useful for my task.
Sorry if this question seems stupid, I'm new to bioinformatics :)