A biologist’s guide to Bayesian phylogenetic analysis

Does the choice of nucleotide substitution models matter topologically?

(2016) Michael Hoff et al.   BMC BIOINFORMATICS

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Deformed wing virus is a recent global epidemic in honeybees driven by Varroa mites

(2016) L. Wilfert et al.   SCIENCE

RevBayes: Bayesian Phylogenetic Inference Using Graphical Models and an Interactive Model-Specification Language

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Challenges in Species Tree Estimation Under the Multispecies Coalescent Model

(2016) Bo Xu et al.   GENETICS

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

Multiple sequence alignment modeling: methods and applications

(2015) Maria Chatzou et al.   BRIEFINGS IN BIOINFORMATICS

Uncertainty in the Timing of Origin of Animals and the Limits of Precision in Molecular Timescales

(2015) Mario dos Reis et al.   CURRENT BIOLOGY

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

Bayesian species delimitation combining multiple genes and traits in a unified framework

(2015) Claudia Solís-Lemus et al.   EVOLUTION

Evolution of endemism on a young tropical mountain

(2015) Vincent S. F. T. Merckx et al.   NATURE

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Bayesian molecular clock dating of species divergences in the genomics era

(2015) Mario dos Reis et al.   NATURE REVIEWS GENETICS

The two-domain tree of life is linked to a new root for the Archaea

(2015) Kasie Raymann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phycas: Software for Bayesian Phylogenetic Analysis

(2015) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

Modeling Character Change Heterogeneity in Phylogenetic Analyses of Morphology through the Use of Priors

(2015) April M. Wright et al.   SYSTEMATIC BIOLOGY

Dating Tips for Divergence-Time Estimation

(2015) Joseph E. O’Reilly et al.   TRENDS IN GENETICS

RNA Virus Reassortment: An Evolutionary Mechanism for Host Jumps and Immune Evasion

(2015) Dhanasekaran Vijaykrishna et al.   PLoS Pathogens

The BPP program for species tree estimation and species delimitation

(2015) Ziheng Yang   Current Zoology

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

The fossilized birth-death process for coherent calibration of divergence-time estimates

(2014) T. A. Heath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The early spread and epidemic ignition of HIV-1 in human populations

(2014) N. R. Faria et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The Impact of the Rate Prior on Bayesian Estimation of Divergence Times with Multiple Loci

(2014) Mario Dos Reis et al.   SYSTEMATIC BIOLOGY

The Inference of Gene Trees with Species Trees

(2014) Gergely J. Szöllősi et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Searching for efficient Markov chain Monte Carlo proposal kernels

(2013) Z. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Unifying the spatial epidemiology and molecular evolution of emerging epidemics

(2012) O. G. Pybus et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

(2011) B. Rannala et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

(2010) P. Lemey et al.   MOLECULAR BIOLOGY AND EVOLUTION

Amazonia Through Time: Andean Uplift, Climate Change, Landscape Evolution, and Biodiversity

(2010) C. Hoorn et al.   SCIENCE

Three roads diverged? Routes to phylogeographic inference

(2010) Erik W. Bloomquist et al.   TRENDS IN ECOLOGY & EVOLUTION

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Uniting Alignments and Trees

(2009) A. Loytynoja et al.   SCIENCE

When Trees Grow Too Long: Investigating the Causes of Highly Inaccurate Bayesian Branch-Length Estimates

(2009) Jeremy M. Brown et al.   SYSTEMATIC BIOLOGY

Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times

(2009) Simon Y. W. Ho et al.   SYSTEMATIC BIOLOGY

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY