PAML

PAML, which stands for Phylogenetic Analysis by Maximum Likelihood, is a software package widely used in bioinformatics for phylogenetic inference and evolutionary analysis. It provides a suite of programs designed to perform various evolutionary analyses, with a particular focus on methods that utilize the maximum likelihood framework. Developed by Ziheng Yang, PAML is highly regarded for its flexibility and its ability to handle complex evolutionary models.

The core functionality of PAML revolves around estimating phylogenetic trees and analyzing evolutionary rates and patterns. It can infer evolutionary relationships between DNA, RNA, or protein sequences by fitting various statistical models of molecular evolution to the data. These models account for factors such as different substitution rates between nucleotides or amino acids, codon usage bias, and the presence of positive selection.

PAML offers several programs, each tailored for specific types of analyses. For instance, BASEML is used for constructing phylogenetic trees under the basic substitution models. CODEML is a powerful program for analyzing codon sequences, enabling the detection of positive selection (dN/dS ratios greater than 1) and the estimation of evolutionary rates at the codon level. Other programs within the suite facilitate analyses such as divergence time estimation and molecular dating. Its robust implementation of maximum likelihood methods makes it a valuable tool for researchers studying molecular evolution, population genetics, and comparative genomics.