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 …

As the amount of molecular sequence data in the public domain grows, so does the range of
biological topics that it influences through evolutionary considerations. In recent years, a …

Resolving the relationships between the major lineages in the animal tree of life is
necessary to understand the origin and evolution of key animal traits. Sponges …

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML
versions used a fast algorithm performing nearest neighbor interchanges to improve a …

Motivation: As high-throughput transcriptome sequencing provides evidence for novel
transcripts in many species, there is a renewed need for accurate methods to classify small …

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 …

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 …

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 …