Beginner's Guide on the Use of PAML to Detect Positive Selection

The CODEML program in the PAML package has been widely used to analyze protein-coding gene sequences to estimate the synonymous and nonsynonymous rates (dS and dN) and to detect positive Darwinian selection driving protein evolution. For users not familiar with molecular evolutionary analysis, the program is known to have a steep learning curve. Here, we provide a step-by-step protocol to illustrate the commonly used tests available in the program, including the branch models, the site models, and the branch-site models, which can be used to detect positive selection driving adaptive protein evolution affecting particular lineages of the species phylogeny, affecting a subset of amino acid residues in the…

• DF
  Directorate for Biological Sciences
• BA
  Biotechnology and Biological Sciences Research Council

  Awards: BB/R01356X/1, BB/T012951/1, BB/R01356X/1, BB/R016240/1, BB/R016240/1, BB/T012951/1