Hello, everyone, I'm trying to understand how to run codeml to detect positive selection gene and sites with certain lineages. But still two question make me much confused: Question One: how can I obtain initial kappa value and initial omega value? Running M0 model(model=0,Nsites=0) firstly for obtaining these value and then running model what I need? and how about setting up of fix_kappa and fix_omega? Question Two: As Yang's paper said(About PAML published on 2007), PAML can detect relationship between gene duplication and selective pressure by branch and branch-site model. However, some duplicated genes will not located within branches which their paralog
located in because there has already sequence diversification in duplicated genes, so how can I set foreground branch if I wanna detect selective pressure of genes in the duplicated gene families? Thanks for your kindly help!