Abstract

PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate con-stancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of sub-stitution rates at sites and reconstruction of ancestral nucleo-tide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.