BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Bayesian reconstruction of transmission within outbreaks using genomic variants

(2018) Nicola De Maio et al.   PLoS Computational Biology

Local and relaxed clocks: the best of both worlds

(2018) Mathieu Fourment et al.   PeerJ

P3: Phylogenetic Posterior Prediction in RevBayes

(2017) Sebastian Höhna et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

StarBEAST2 Brings Faster Species Tree Inference and Accurate Estimates of Substitution Rates

(2017) Huw A. Ogilvie et al.   MOLECULAR BIOLOGY AND EVOLUTION

Why Concatenation Fails Near the Anomaly Zone

(2017) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Taming the BEAST—A Community Teaching Material Resource for BEAST 2

(2017) Joëlle Barido-Sottani et al.   SYSTEMATIC BIOLOGY

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data

(2016) Timothy G. Vaughan et al.   GENETICS

Algorithmic improvements to species delimitation and phylogeny estimation under the multispecies coalescent

(2016) Graham Jones   JOURNAL OF MATHEMATICAL BIOLOGY

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

(2016) Hugo F. Gante et al.   MOLECULAR ECOLOGY

Evolution of the immune system influences speciation rates in teleost fishes

(2016) Martin Malmstrøm et al.   NATURE GENETICS

After Ebola in West Africa — Unpredictable Risks, Preventable Epidemics

(2016)   NEW ENGLAND JOURNAL OF MEDICINE

Fungal-algal association patterns in lichen symbiosis linked to macroclimate

(2016) Garima Singh et al.   NEW PHYTOLOGIST

Gene Tree Discordance Causes Apparent Substitution Rate Variation

(2016) Fábio K. Mendes et al.   SYSTEMATIC BIOLOGY

Computational Performance and Statistical Accuracy of *BEAST and Comparisons with Other Methods

(2016) Huw A. Ogilvie et al.   SYSTEMATIC BIOLOGY

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

(2016) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

Inferring Ancestral Recombination Graphs from Bacterial Genomic Data

(2016) Timothy G. Vaughan et al.   GENETICS

Phylogeography by diffusion on a sphere: whole world phylogeography

(2016) Remco Bouckaert   PeerJ

West African Ebola Epidemic after One Year — Slowing but Not Yet under Control

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Total-Evidence Dating under the Fossilized Birth–Death Process

(2015) Chi Zhang et al.   SYSTEMATIC BIOLOGY

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

(2015) Nicola De Maio et al.   SYSTEMATIC BIOLOGY

Which Phylogenetic Networks are Merely Trees with Additional Arcs?

(2015) Andrew R. Francis et al.   SYSTEMATIC BIOLOGY

Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent

(2015) Sebastien Roch et al.   THEORETICAL POPULATION BIOLOGY

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

DISSECT: an assignment-free Bayesian discovery method for species delimitation under the multispecies coalescent

(2014) Graham Jones et al.   BIOINFORMATICS

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

Infectious disease: Tough choices to reduce Ebola transmission

(2014) Christopher J. M. Whitty et al.   NATURE

The genomic substrate for adaptive radiation in African cichlid fish

(2014) David Brawand et al.   NATURE

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

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Inference of Sampled Ancestor Trees for Epidemiology and Fossil Calibration

(2014) Alexandra Gavryushkina et al.   PLoS Computational Biology

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Evolutionary rates and HBV: issues of rate estimation with Bayesian molecular methods

(2013) Remco Bouckaert et al.   ANTIVIRAL THERAPY

Linking Great Apes Genome Evolution across Time Scales Using Polymorphism-Aware Phylogenetic Models

(2013) Nicola De Maio et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Stochastic Simulator of Birth-Death Master Equations with Application to Phylodynamics

(2013) T. G. Vaughan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Posterior Predictive Bayesian Phylogenetic Model Selection

(2013) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

The Influence of Gene Flow on Species Tree Estimation: A Simulation Study

(2013) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)

(2012) T. Stadler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Origins and Expansion of the Indo-European Language Family

(2012) R. Bouckaert et al.   SCIENCE

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

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo

(2011) Chieh-Hsi Wu et al.   GENETICS

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference of human population history from individual whole-genome sequences

(2011) Heng Li et al.   NATURE

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Divergence Time Estimation Using Fossils as Terminal Taxa and the Origins of Lissamphibia

(2011) R. Alexander Pyron   SYSTEMATIC BIOLOGY

Bayesian random local clocks, or one rate to rule them all

(2010) Alexei J Drummond et al.   BMC BIOLOGY

Sampling-through-time in birth–death trees

(2010) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

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

Choosing among Partition Models in Bayesian Phylogenetics

(2010) Y. Fan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

On incomplete sampling under birth–death models and connections to the sampling-based coalescent

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework

(2009) Erik W. Bloomquist et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Bayesian inference of fine-scale recombination rates using population genomic data

(2008) Y. Wang et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES