PAML is a program package for phylogenetic analysis using maximum likelihood (ML). It is designed for DNA and protein sequence analysis, offering various functions such as estimating evolutionary parameters, testing hypotheses about sequence evolution, calculating substitution rates, reconstructing ancestral sequences, and phylogenetic tree reconstruction. PAML implements a variety of evolutionary models, including models for variable rates among sites, combined analysis of multiple gene sequences, and amino acid sequences. It supports multifurcating trees and trees with ancestral relationships. Although the package uses a heuristic tree search algorithm, tree construction is not a strong point of the current version. Major programs and their functions are listed in Table 1. PAML is freely available for academic use and can be downloaded via anonymous ftp or the World Wide Web. It includes source code, documentation, example data sets, and control files. The package is supported by grants from the National Science Foundation of China, NSF, and NIH. The authors acknowledge contributions from various individuals and institutions. References to related studies are provided. PAML is a powerful tool for phylogenetic analysis due to its comprehensive set of models and functions.PAML is a program package for phylogenetic analysis using maximum likelihood (ML). It is designed for DNA and protein sequence analysis, offering various functions such as estimating evolutionary parameters, testing hypotheses about sequence evolution, calculating substitution rates, reconstructing ancestral sequences, and phylogenetic tree reconstruction. PAML implements a variety of evolutionary models, including models for variable rates among sites, combined analysis of multiple gene sequences, and amino acid sequences. It supports multifurcating trees and trees with ancestral relationships. Although the package uses a heuristic tree search algorithm, tree construction is not a strong point of the current version. Major programs and their functions are listed in Table 1. PAML is freely available for academic use and can be downloaded via anonymous ftp or the World Wide Web. It includes source code, documentation, example data sets, and control files. The package is supported by grants from the National Science Foundation of China, NSF, and NIH. The authors acknowledge contributions from various individuals and institutions. References to related studies are provided. PAML is a powerful tool for phylogenetic analysis due to its comprehensive set of models and functions.