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.

Keywords

Coalescent theoryPhylogenetic treeMarkov chain Monte CarloBayesian probabilityComputer scienceBayesian inferenceEvolutionary biologyInferenceDivergence (linguistics)Data miningArtificial intelligenceMachine learningBiology

Affiliated Institutions

Related Publications

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

Alexei J. Drummond , Marc A. Suchard , Dong Xie +1 more

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of mol...

2012 Molecular Biology and Evolution 10198 citations

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

Vladimir N. Minin , Erik Bloomquist , Marc A. Suchard

Kingman's coalescent process opens the door for estimation of population genetics model parameters from molecular sequences. One paramount parameter of interest is the effective...

2008 Molecular Biology and Evolution 735 citations

Estimating Mutation Parameters, Population History and Genealogy Simultaneously From Temporally Spaced Sequence Data

Alexei J. Drummond , Geoff K. Nicholls , Allen G. Rodrigo +1 more

Abstract Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly a...

2002 Genetics 1077 citations

Bayesian Inference of Species Trees from Multilocus Data

Joseph Heled , Alexei J. Drummond

Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With te...

2009 Molecular Biology and Evolution 2497 citations

Joint Inference of Microsatellite Mutation Models, Population History and Genealogies Using Transdimensional Markov Chain Monte Carlo

Chieh‐Hsi Wu , Alexei J. Drummond

Abstract We provide a framework for Bayesian coalescent inference from microsatellite data that enables inference of population history parameters averaged over microsatellite m...

2011 Genetics 86 citations

Publication Info

Year: 2018
Type: article
Volume: 4
Issue: 1
Pages: vey016-vey016
Citations: 3725
Access: Closed

External Links

View on DOI.org

Social Impact

Altmetric

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

PlumX Metrics

Social media, news, blog, policy document mentions

Citation Metrics

3725

OpenAlex

Cite This

APA Style

                            
                                
                                    Marc A. Suchard, 
                                
                                    Philippe Lemey, 
                                
                                    Guy Baele
                                
                                et al.
                            
                            (2018). 
                            Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. 
                            Virus Evolution
                            , 4
                            (1)
                            , vey016-vey016.
                            https://doi.org/10.1093/ve/vey016
                        

Identifiers

DOI: 10.1093/ve/vey016