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Major revisions in pancrustacean phylogeny and evidence of sensitivity to taxon sampling
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 …
of animals on earth, containing over 80% of animal species and half of animal biomass. It …
A review of long‐branch attraction
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 …
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
Big, time-scaled phylogenies are fundamental to connecting evolutionary processes to
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …
modern biodiversity patterns. Yet inferring reliable phylogenetic trees for thousands of …
RevBayes: Bayesian phylogenetic inference using graphical models and an interactive model-specification language
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 …
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
Phylogenetic inference and evaluating support for inferred relationships is at the core of
many studies testing evolutionary hypotheses. Despite the popularity of nonparametric …
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
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 …
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
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 …
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
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 …
the same substitution process, characterized by a 20× 20 substitution matrix. Here, we …
Bayesian phylogenetic analysis of combined data
The recent development of Bayesian phylogenetic inference using Markov chain Monte
Carlo (MCMC) techniques has facilitated the exploration of parameter-rich evolutionary …
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
Motivation: The computation of large phylogenetic trees with statistical models such as
maximum likelihood or bayesian inference is computationally extremely intensive. It has …
maximum likelihood or bayesian inference is computationally extremely intensive. It has …