Hi everyone, I am trying to do selection analysis on one particular gene and I have sequences of that gene from about 130 species. Out of these 130, about 30 are from one group and 100 from another group. Let us call them group A (30 species) and group B (100) I want to compare dN/dS values and sites which have undergone episodic selection between these two groups. My question is whether I should align these two groups separately and run analysis separately or would it be better if I have one alignment file which I should give FEL and choose A as foreground and B as background? I am new to this and I am confused as to which is a better approach.

Thanks for your help in advance.