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 construction of evolutionary trees is now a standard part of exploratory sequence
analysis. Bayesian methods for estimating trees have recently been proposed as a faster …

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 …

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 …

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 …

Escherichia coli is a model laboratory bacterium, a species that is widely distributed in the
environment, as well as a mutualist and pathogen in its human hosts. As such, E. coli …

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

Studies of evolution at the molecular level have experienced phenomenal growth in the last
few decades, due to rapid accumulation of genetic sequence data, improved computer …

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 …