PAML 4: phylogenetic analysis by maximum likelihood

PAML, currently in version 4, is a package of programs for phylogeneticanalyses of DNA and protein sequences using maximum likelihood(ML). The programs may be used to compare and test phylogenetictrees, but their main strengths lie in the rich repertoire ofevolutionary models implemented, which can be used to estimateparameters in models of sequence evolution and to test interestingbiological hypotheses. Uses of the programs include estimationof synonymous and nonsynonymous rates (d_N and d_S) between twoprotein-coding DNA sequences, inference of positive Darwinianselection through phylogenetic comparison of protein-codinggenes, reconstruction of ancestral genes and proteins for molecularrestoration studies of extinct life forms, combined analysisof heterogeneous data sets from multiple gene loci, and estimationof species divergence times incorporating uncertainties in fossilcalibrations. This note discusses some of the major applicationsof the package, which includes example data sets to demonstratetheir use. The package is written in ANSI C, and runs underWindows, Mac OSX, and UNIX systems. It is available at http://abacus.gene.ucl.ac.uk/software/paml.html.