Approximate methods for estimating the numbers of synonymous and nonsynonymous
substitutions between two DNA sequences involve three steps: counting of synonymous and …

A novel test is described that visualizes the absolute model-data fit of the substitution and
tree components of an evolutionary model. The test utilizes statistics based on counts of …

The use of parameter-rich substitution models in molecular phylogenetics has been
criticized on the basis that these models can cause a reduction both in accuracy and in the …

We test models for the evolution of helical regions of RNA sequences, where the base
pairing constraint leads to correlated compensatory substitutions occurring on either side of …

The non-homogeneous model of nucleotide substitution proposed by Barry and Hartigan
(Stat Sci, 2: 191–210) is the most general model of DNA evolution assuming an independent …

Traditional approaches to probabilistic phylogenetic inference have relied on information-
theoretic criteria to select among a relatively small set of substitution models. These model …

Despite the relevant role of models of nucleotide substitution in phylogenetics, choosing
among different models remains a problem. Several statistical methods for selecting the …

The loss of information accompanying assessment of absolute fit of substitution models to
phylogenetic data negatively affects the discriminatory power of previous methods and can …

Abstract Models of codon substitution have been commonly used to compare protein-coding
DNA sequences and are particularly effective in detecting signals of natural selection acting …

Phylogenetic analyses of DNA sequence data can provide estimates of evolutionary rates
and timescales. Nearly all phylogenetic methods rely on accurate models of nucleotide …