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

Inferring Speciation and Extinction Rates under Different Sampling Schemes

(2011) S. Hohna 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

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Bayesian Phylogenetics and Its Influence on Insect Systematics

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

Examples of Adaptive MCMC

(2009) Gareth O. Roberts et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

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

(2009) Tanja Stadler   JOURNAL OF THEORETICAL BIOLOGY

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

The conditioned reconstructed process

(2008) Tanja Gernhard   JOURNAL OF THEORETICAL BIOLOGY

jModelTest: Phylogenetic Model Averaging

(2008) D. Posada   MOLECULAR BIOLOGY AND EVOLUTION

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY