CODEML

CODEML is a software program used for phylogenetic analysis, specifically for detecting positive selection in protein-coding genes. It is part of the PAML (Phylogenetic Analysis by Maximum Likelihood) package, a widely used suite of programs for molecular evolution. CODEML implements various models of molecular evolution that allow researchers to estimate the ratio of nonsynonymous to synonymous substitution rates, often denoted as omega ($\omega$).

A value of $\omega > 1$ suggests positive selection, where advantageous mutations are accumulating in a lineage. Conversely, $\omega < 1$ indicates purifying selection, meaning that most mutations are deleterious and are being removed by selection. $\omega = 1$ suggests neutral evolution. CODEML offers several site-specific models, branch-specific models, and branch-site models to investigate selection pressures across different parts of a gene and along different evolutionary lineages. The program requires aligned DNA or protein sequences and a corresponding phylogenetic tree as input. Its output includes likelihood scores for different selection models, estimated $\omega$ values, and lists of sites potentially under selection, which are crucial for understanding the evolutionary forces shaping gene function and adaptation.