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

Phycas: Software for Bayesian Phylogenetic Analysis

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

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

Probabilistic Graphical Model Representation in Phylogenetics

(2014) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters

(2014) Luke B. Harrison et al.   SYSTEMATIC BIOLOGY

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral Sequences

(2013) M. Groussin et al.   SYSTEMATIC BIOLOGY

Bayesian Analysis of Biogeography when the Number of Areas is Large

(2013) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogenetics: principles and practice

(2012) Ziheng Yang et al.   NATURE REVIEWS GENETICS

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

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

Phylogenetic Analysis Using Lévy Processes: Finding Jumps in the Evolution of Continuous Traits

(2012) Michael J. Landis et al.   SYSTEMATIC BIOLOGY

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

A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates

(2011) T. A. Heath et al.   MOLECULAR BIOLOGY AND EVOLUTION

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

(2011) Daniel L. Ayres et al.   SYSTEMATIC BIOLOGY

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

(2010) Alexei J Drummond et al.   BMC BIOLOGY

A Phylogenetic Model for Investigating Correlated Evolution of Substitution Rates and Continuous Phenotypic Characters

(2010) N. Lartillot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics and Its Influence on Insect Systematics

(2009) Fredrik Ronquist et al.   Annual Review of Entomology

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

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

The BUGS project: Evolution, critique and future directions

(2009) David Lunn et al.   STATISTICS IN MEDICINE

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Inferring dispersal: a Bayesian approach to phylogeny-based island biogeography, with special reference to the Canary Islands

(2008) Isabel Sanmartín et al.   JOURNAL OF BIOGEOGRAPHY

Parallel adaptations to high temperatures in the Archaean eon

(2008) Bastien Boussau et al.   NATURE

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY