Dear All, I have a lineage that is all parasitic plant sequences, I want to examine inside the sequences, if there are sites evolving under positive selection.
Now I have a tree file, which is a parasitic-plant lineage and some other sequences (from several legume species). This is a part of a tree reflecting horizontal gene transfer. We detected that our parasitic plants got this gene from its host Medicago(non parasitic plants). We are very interested in identifying if sequences in the parasites have some sites that evolve some new function. However, because this sequences are very similar, so on the whole sequence level, Ks/Ks < 1, suggesting it evolves some negative selection. So I was wondering if there are particular sites under positive selection.
I use the following major parameters in my .ctl file fix_kappa = 0 * 1: kappa fixed, 0: kappa to be estimated kappa = .3 * initial or fixed kappa fix_omega = 0 * 1: omega or omega_1 fixed, 0: estimate omega = 1.3 * initial or fixed omega, for codons or codon-based AAs ncatG = 10 * # of categories in the dG or AdG models of rates
I am not sure if my settings are correct. If anyone can give me some suggestions on how to do this in paml or give me some suggestions, I would appreciate it a lot. I run this in paml it seems that there is no positively selected sites, yet I am not sure.
Anyone has some experience in identifying sites under positive selection for a particular lineage? Suggestions are welcome!