PAML (Program for Analysis of Molecular Evolution) is a software package for phylogenetic analysis of DNA and protein sequences using maximum likelihood (ML) methods. Version 1.2 of PAML offers several functionalities, including ML estimation of evolutionary parameters, likelihood ratio tests for sequence evolution hypotheses, calculation of substitution rates, and phylogenetic tree reconstruction. The package supports various evolutionary models, such as variable rates among sites, combined analyses of multiple gene sequences, and amino acid sequences. It also handles multifurcating trees and ancestral sequences. PAML uses a heuristic tree search algorithm but lacks efficient tree-making capabilities. The software is freely available for academic use and can be obtained via anonymous FTP or from the World Wide Web. The development of PAML was supported by grants from the National Science Foundation of China, NSF, and NIH.PAML (Program for Analysis of Molecular Evolution) is a software package for phylogenetic analysis of DNA and protein sequences using maximum likelihood (ML) methods. Version 1.2 of PAML offers several functionalities, including ML estimation of evolutionary parameters, likelihood ratio tests for sequence evolution hypotheses, calculation of substitution rates, and phylogenetic tree reconstruction. The package supports various evolutionary models, such as variable rates among sites, combined analyses of multiple gene sequences, and amino acid sequences. It also handles multifurcating trees and ancestral sequences. PAML uses a heuristic tree search algorithm but lacks efficient tree-making capabilities. The software is freely available for academic use and can be obtained via anonymous FTP or from the World Wide Web. The development of PAML was supported by grants from the National Science Foundation of China, NSF, and NIH.