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A codon-based model for the evolution of protein-coding DNA sequences is presented
for use in phylogenetic estimation. A Markov process is used to describe substitutions
between codons. Transition/transversion rate bias and codon usage bias are allowed
in the model, and selective restraints at the protein level are accommodated using
physicochemical distances between the amino acids coded for by the codons. Analyses
of two data sets suggest that the new codon-based model can provide a better fit to
data than can nucleotide-based models and can produce more reliable estimates of certain
biologically important measures such as the transition/transversion rate ratio and
the synonymous/nonsynonymous substitution rate ratio.