19 Dubious Ways to Compute the Marginal Likelihood of a Phylogenetic Tree Topology

Stochastic Variational Inference for Bayesian Phylogenetics: A Case of CAT Model

(2019) Tung Dang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic Exploration of the High Likelihood Set of Phylogenetic Tree Topologies

(2019) Chris Whidden et al.   SYSTEMATIC BIOLOGY

Model selection and parameter inference in phylogenetics using Nested Sampling

(2018) Patricio Maturana R et al.   SYSTEMATIC BIOLOGY

A tutorial on bridge sampling

(2017) Quentin F. Gronau et al.   JOURNAL OF MATHEMATICAL PSYCHOLOGY

Practical Bayesian model evaluation using leave-one-out cross-validation and WAIC

(2016) Aki Vehtari et al.   STATISTICS AND COMPUTING

Estimating Bayesian Phylogenetic Information Content

(2016) Paul O. Lewis et al.   SYSTEMATIC BIOLOGY

An Efficient Independence Sampler for Updating Branches in Bayesian Markov chain Monte Carlo Sampling of Phylogenetic Trees

(2015) Andre J. Aberer et al.   SYSTEMATIC BIOLOGY

Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty

(2015) Guy Baele et al.   SYSTEMATIC BIOLOGY

Quantifying MCMC Exploration of Phylogenetic Tree Space

(2015) Chris Whidden et al.   SYSTEMATIC BIOLOGY

Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data

(2014) Mathieu Fourment et al.   BMC EVOLUTIONARY BIOLOGY

Posterior Predictive Bayesian Phylogenetic Model Selection

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

The Estimation of Tree Posterior Probabilities Using Conditional Clade Probability Distributions

(2013) Bret Larget   SYSTEMATIC BIOLOGY

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths

(2012) Chi Zhang 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

Approximate Likelihood Calculation on a Phylogeny for Bayesian Estimation of Divergence Times

(2011) M. d. Reis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference

(2011) B. Rannala et al.   MOLECULAR BIOLOGY AND EVOLUTION

Guided Tree Topology Proposals for Bayesian Phylogenetic Inference

(2011) Sebastian Höhna et al.   SYSTEMATIC BIOLOGY

Default Bayesian model determination methods for generalised linear mixed models

(2010) Antony M. Overstall et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

Computational Aspects Related to Inference in Gaussian Graphical Models With the G-Wishart Prior

(2010) Alex Lenkoski et al.   JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS

Bayesian Estimation of Divergence Times from Large Sequence Alignments

(2010) S. Guindon   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

Marginal likelihood estimation via power posteriors

(2008) N. Friel et al.   JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY

Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics

(2008) Clemens Lakner et al.   SYSTEMATIC BIOLOGY