Bayesian Phylogenetics with BEAUti and the BEAST 1.7

SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics

(2011) F. Bielejec et al.   BIOINFORMATICS

Model Averaging and Bayes Factor Calculation of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2011) W. L. S. Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled 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

CALIBRATING DIVERGENCE TIMES ON SPECIES TREES VERSUS GENE TREES: IMPLICATIONS FOR SPECIATION HISTORY OF APHELOCOMA JAYS

(2010) John E. McCormack et al.   EVOLUTION

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

A Bayesian Phylogenetic Method to Estimate Unknown Sequence Ages

(2010) B. Shapiro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Many-core algorithms for statistical phylogenetics

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

Learning to Count: Robust Estimates for Labeled Distances between Molecular Sequences

(2009) J. D. O'Brien et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

Accommodating the Effect of Ancient DNA Damage on Inferences of Demographic Histories

(2008) A. Rambaut et al.   MOLECULAR BIOLOGY AND EVOLUTION

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