Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Abstract The Bayesian Evolutionary Analysis by Sampling Trees (BEAST) software package has become a primary tool for Bayesian phylogenetic and phylodynamic inference from genetic sequence data. BEAST unifies molecular phylogenetic reconstruction with complex discrete and continuous trait evolution, divergence-time dating, and coalescent demographic models in an efficient statistical inference engine using Markov chain Monte Carlo integration. A convenient, cross-platform, graphical user interface allows the flexible construction of complex evolutionary analyses.

[1]  H. Philippe,et al.  Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.

[2]  Richard A Neher,et al.  TreeTime: Maximum-likelihood phylodynamic analysis , 2017, bioRxiv.

[3]  Ming-Hui Chen,et al.  Improving marginal likelihood estimation for Bayesian phylogenetic model selection. , 2011, Systematic biology.

[4]  Guy Baele,et al.  Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation , 2016, Microbial genomics.

[5]  M. Suchard,et al.  Phylogeography takes a relaxed random walk in continuous space and time. , 2010, Molecular biology and evolution.

[6]  O. Pybus,et al.  Unifying the Epidemiological and Evolutionary Dynamics of Pathogens , 2004, Science.

[7]  Marc A Suchard,et al.  Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates. , 2016, Systematic biology.

[8]  Guy Baele,et al.  Adaptive MCMC in Bayesian phylogenetics: an application to analyzing partitioned data in BEAST , 2017, Bioinform..

[9]  M. Suchard,et al.  Bayesian Phylogenetics with BEAUti and the BEAST 1.7 , 2012, Molecular biology and evolution.

[10]  Erik M. Volz,et al.  Scalable relaxed clock phylogenetic dating , 2017 .

[11]  M. Suchard,et al.  Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2 , 2014, PLoS pathogens.

[12]  A. Lapedes,et al.  Mapping the Antigenic and Genetic Evolution of Influenza Virus , 2004, Science.

[13]  Trevor Bedford,et al.  Virus genomes reveal factors that spread and sustained the Ebola epidemic , 2017, Nature.

[14]  Matthew Hall,et al.  Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set , 2014, PLoS Comput. Biol..

[15]  Trevor Bedford,et al.  Integrating influenza antigenic dynamics with molecular evolution , 2013, eLife.

[16]  Dong Xie,et al.  BEAST 2: A Software Platform for Bayesian Evolutionary Analysis , 2014, PLoS Comput. Biol..

[17]  Marc A Suchard,et al.  Fast, accurate and simulation-free stochastic mapping , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[18]  Guy Baele,et al.  The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates , 2014, PLoS Comput. Biol..

[19]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.

[20]  Olivier Gascuel,et al.  Fast Dating Using Least-Squares Criteria and Algorithms , 2015, Systematic biology.

[21]  Vladimir N. Minin,et al.  A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection , 2012, Bioinform..

[22]  Ming-Hui Chen,et al.  Choosing among Partition Models in Bayesian Phylogenetics , 2010, Molecular biology and evolution.

[23]  M. Suchard,et al.  SpreaD3: Interactive Visualization of Spatiotemporal History and Trait Evolutionary Processes. , 2016, Molecular biology and evolution.

[24]  Max R. Tolkoff,et al.  Phylogenetic Factor Analysis. , 2017, Systematic biology.

[25]  Guy Baele,et al.  Identifying predictors of time-inhomogeneous viral evolutionary processes , 2016, Virus evolution.

[26]  Xiao-Li Meng,et al.  Simulating Normalizing Constants: From Importance Sampling to Bridge Sampling to Path Sampling , 1998 .

[27]  Mandev S. Gill,et al.  A Relaxed Directional Random Walk Model for Phylogenetic Trait Evolution. , 2016, Systematic biology.

[28]  Trevor Bedford,et al.  ASSESSING PHENOTYPIC CORRELATION THROUGH THE MULTIVARIATE PHYLOGENETIC LATENT LIABILITY MODEL. , 2014, The annals of applied statistics.

[29]  Daniel L. Ayres,et al.  BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics , 2011, Systematic biology.

[30]  M. Suchard,et al.  Hierarchical phylogenetic models for analyzing multipartite sequence data. , 2003, Systematic biology.

[31]  M. Suchard,et al.  Genealogical Working Distributions for Bayesian Model Testing with Phylogenetic Uncertainty. , 2016, Systematic biology.

[32]  M. Suchard,et al.  Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. , 2012, Molecular biology and evolution.