How should ecologists and evolutionary biologists analyze nonnormal data that involve
random effects? Nonnormal data such as counts or proportions often defy classical statistical …

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 …

The program MODELTEST uses log likelihood scores to establish the model of DNA
evolution that best fits the data. AVAILABILITY: The MODELTEST package, including the …

Abstract Model selection is a topic of special relevance in molecular phylogenetics that
affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental …

This book is both a manual for the computer program MacClade, describing its features and
potential uses, as well as a portrayal of a phylogenetic approach to studying diversity and …

We revisit statistical tests for branches of evolutionary trees reconstructed upon molecular
data. A new, fast, approximate likelihood-ratio test (aLRT) for branches is presented here as …

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 selective pressure at the protein level is usually measured by the nonsynonymous/
synonymous rate ratio (ω= d N/d S), with ω< 1, ω= 1, and ω> 1 indicating purifying (or …

Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies)
have been available for approximately a decade. By far the most commonly used is the …

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 …