Phylogenetic Analysis By Maximum Likelihood (Paml): how to use the app

Question

[katyaspasiyk2002]

Dear all, I want to use PAML for Checking positive selection by dn/ds calculation. I have pooled 13 protein-coding genes for 49 insect species. The problem is that I can't figure out how to calculate Dn/Ds to end up with a table with Dn/Ds values for each species or taxon. I tried Mega 7, but it only produces a table by codons, not by species or taxon. You need a table like the one in the picture. enter link description hereCombining and aligning sequences was done in Mega 7.

Answer 1

[shelkmike]

You need to run Codeml providing your alignment and a phylogenetic tree as input. You need to use the free-ratios model by indicating "model = 1" in the config file of Codeml. In the phylogenetic tree you need to mark all branches that belong to a specific taxon. For example, mark by "#0" all branches that belong to Psocoptera, by "#1" all branches that belong to Thysanoptera, etc. The results that you need will be at the end of the file produced by Codeml. For more details, read the manual for Codeml (http://abacus.gene.ucl.ac.uk/software/pamlDOC.pdf). PAML is not the simplest program (sometimes I call it "facepaml"), which means that you need to read the manual especially carefully.

[katyaspasiyk2002]

codeml is like a supplement to the PAML program? Does it all need to be downloaded to your computer? Maybe you can suggest some alternatives to this program that can calculate, I'm afraid I can't figure it out(((

[shelkmike]

Codeml is a part of PAML. PAML is actually not a single program, but a suite of programs.

There are, I think, no simple alternatives to PAML for what you want to do. You may try PhyML, but it's not much simpler than PAML. Anyway, you'll have to spend some time to solve your task.