Phylogenetic Analysis by Maximum Likelihood (PAML) PAML is a program package for phylogenetic analyses of DNA or protein sequences using maximum likelihood, and is maintained and distributed by Ziheng Yang. Possible uses of the programs are: - Estimation of branch lengths in a phylogenetic tree and parameters in the evolutionary model such as the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates among sites, and rate parameters for different genes; - Test of hypotheses concerning sequence evolution, such as rate constancy and independence among nucleotide or amino acid sites, rate constancy among lineages (the molecular clock), and homogeneity of evolutionary process in multiple genes; - Calculation of substitution rates at sites; - Reconstruction of ancestral nucleotide or amino acid sequences; - Simulation of nucleotide, codon, and amino acid sequence data sets; - Phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.