I am trying to calculate dN/dS ratio for protein coding genes. I have sequence alignment for a protein coding gene for about 30 species that includes an outgroup. I do not have much experience on using PAML package. I am familiar with tweaking parameters in codeml.ctl file for different models - site, branch, and branch site. However, I am not sure what kind of analysis would be better to get dN and dS values for each species in the alignment. I tired model = 1 and got branch specific dN/dS values but I am not sure branch specific omega values corresponds to omega value for each species. Or would it be better to do pairwise comparison using runmode = -2 and look at dN/dS value compare to outgroup?
It would be great to get some help with interpreting results.