BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

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

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

(2013) Remco Bouckaert et al.   ANTIVIRAL THERAPY

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

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

Bayesian Selection of Nucleotide Substitution Models and Their Site Assignments

(2012) Chieh-Hsi Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

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

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

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

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

DensiTree: making sense of sets of phylogenetic trees

(2010) R. R. Bouckaert   BIOINFORMATICS

Phylogeography Takes a Relaxed Random Walk in Continuous Space and Time

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

Many-core algorithms for statistical phylogenetics

(2009) M. A. Suchard et al.   BIOINFORMATICS

Evidence of a Large, International Network of HCV Transmission in HIV-Positive Men Who Have Sex With Men

(2009) Thijis van de Laar et al.   GASTROENTEROLOGY

Bayesian Inference of Species Trees from Multilocus Data

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

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Bayesian inference of population size history from multiple loci

(2008) Joseph Heled et al.   BMC EVOLUTIONARY BIOLOGY

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Wagner and Dollo: A Stochastic Duet by Composing Two Parsimonious Solos

(2008) Alexander V. Alekseyenko et al.   SYSTEMATIC BIOLOGY