Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling

JP Bernot, CL Owen, JM Wolfe, K Meland… - Molecular Biology …, 2023‏ - academic.oup.com
The clade Pancrustacea, comprising crustaceans and hexapods, is the most diverse group
of animals on earth, containing over 80% of animal species and half of animal biomass. It …

A review of long‐branch attraction

J Bergsten - Cladistics, 2005‏ - Wiley Online Library
The history of long‐branch attraction, and in particular methods suggested to detect and
avoid the artifact to date, is reviewed. Methods suggested to avoid LBA‐artifacts include …

Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation

NS Upham, JA Esselstyn, W Jetz - PLoS biology, 2019‏ - journals.plos.org
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …

RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language

S Höhna, MJ Landis, TA Heath, B Boussau… - Systematic …, 2016‏ - academic.oup.com
Programs for Bayesian inference of phylogeny currently implement a unique and fixed suite
of models. Consequently, users of these software packages are simultaneously forced to …

Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes

M Anisimova, M Gil, JF Dufayard, C Dessimoz… - Systematic …, 2011‏ - academic.oup.com
Phylogenetic inference and evaluating support for inferred relationships is at the core of
many studies testing evolutionary hypotheses. Despite the popularity of nonparametric …

Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests

D Posada, TR Buckley - Systematic biology, 2004‏ - academic.oup.com
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 …

Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative

M Anisimova, O Gascuel - Systematic biology, 2006‏ - academic.oup.com
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 …

A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process

N Lartillot, H Philippe - Molecular biology and evolution, 2004‏ - academic.oup.com
Most current models of sequence evolution assume that all sites of a protein evolve under
the same substitution process, characterized by a 20× 20 substitution matrix. Here, we …

Bayesian phylogenetic analysis of combined data

JAA Nylander, F Ronquist, JP Huelsenbeck… - Systematic …, 2004‏ - academic.oup.com
The recent development of Bayesian phylogenetic inference using Markov chain Monte
Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary …

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

A Stamatakis, T Ludwig, H Meier - Bioinformatics, 2005‏ - academic.oup.com
Motivation: The computation of large phylogenetic trees with statistical models such as
maximum likelihood or bayesian inference is computationally extremely intensive. It has …