What is the best codeml model to determine if a gene is undergoing positive, negative or neutral selection? At this point I am not interested …

Hi, I am using the codeml package of the PAML software for positive selection analysis. I have tried to read the manual as well as …

I have found sites under positive selection in both codeml and meme on HyPhy. The confidence is above 95 and 99percent for many sites in …

Hello! I ran codeml branch-site test (null and alternate) on 2118 genes and found that 42 of these are significant and thus, contain sites under …

Hi, I am running codeml on orthogroup tree to determine whether a certain lineage is under positive selection. The way I did is to set …

<p>Dear All !</p> <p>I tried to use codeml to detect positive selection sites along my interested branches (thereafter these branches). First, I performed &quot;two-ratio&quot; model …

Hi all, I am using codeml in PAML (Phylogenetic Analysis by Maximum Likelihood) to test sites under positive selection in a particular lineage. A summary …

Can I ask a question about saturation test for codeml? I am using free-ratio model against single ratio model to test which branch is under …

Hello everyone, I used the branch-site method to detect positive selection in a linea with codeml. Now I would like to be sure that the …

Dear All, Sorry for the novice question. I have gone through the PAML documentation but it is still very confusing for me. I have two …