Abstract paml, currently in version 4, is a package of programs for phylogenetic analyses of
DNA and protein sequences using maximum likelihood (ML). The programs may be used to …

The selective pressure on a protein-coding gene can be measured by comparing silent
(synonymous) and replacement (nonsynonymous) substitution rates. Higher replacement …

We consider three approaches for estimating the rates of nonsynonymous and synonymous
changes at each site in a sequence alignment in order to identify sites under positive or …

Codon-based substitution models have been widely used to identify amino acid sites under
positive selection in comparative analysis of protein-coding DNA sequences. The …

The first class, which we call counting methods, involves estimating the number of
nonsynonymous and synonymous changes that have occurred at each codon throughout …

The field of molecular evolution has experienced explosive growth in recent years due to the
rapid accumulation of genetic sequence data, continuous improvements to computer …

Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene,
and to a small number of lineages in a phylogenetic tree. A popular class of “branch-site” …

Maximum-likelihood methods based on models of codon substitution accounting for
heterogeneous selective pressures across sites have proved to be powerful in detecting …

The branch-site test is a likelihood ratio test to detect positive selection along prespecified
lineages on a phylogeny that affects only a subset of codons in a protein-coding gene, with …

The parsimony method of and the maximum likelihood method developed from the work of
are two widely used methods for detecting positive selection in homologous protein coding …