BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Top Cited Papers
Open Access
- 10 April 2014
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLoS Computational Biology
- Vol. 10 (4), e1003537
- https://doi.org/10.1371/journal.pcbi.1003537
Abstract
We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. This software platform is a re-design of the popular BEAST 1 platform to correct structural deficiencies that became evident as the BEAST 1 software evolved. Key among those deficiencies was the lack of post-deployment extensibility. BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform. This package architecture is showcased with a number of recently published new models encompassing birth-death-sampling tree priors, phylodynamics and model averaging for substitution models and site partitioning. A second major improvement is the ability to read/write the entire state of the MCMC chain to/from disk allowing it to be easily shared between multiple instances of the BEAST software. This facilitates checkpointing and better support for multi-processor and high-end computing extensions. Finally, the functionality in new packages can be easily added to the user interface (BEAUti 2) by a simple XML template-based mechanism because BEAST 2 has been re-designed to provide greater integration between the analysis engine and the user interface so that, for example BEAST and BEAUti use exactly the same XML file format.Keywords
This publication has 28 references indexed in Scilit:
- Birth–death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)Proceedings of the National Academy of Sciences of the United States of America, 2012
- Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic UncertaintyMolecular Biology and Evolution, 2012
- Bayesian Phylogenetics with BEAUti and the BEAST 1.7Molecular Biology and Evolution, 2012
- DensiTree: making sense of sets of phylogenetic treesBioinformatics, 2010
- Phylogeography Takes a Relaxed Random Walk in Continuous Space and TimeMolecular Biology and Evolution, 2010
- Bayesian Inference of Species Trees from Multilocus DataMolecular Biology and Evolution, 2009
- Many-core algorithms for statistical phylogeneticsBioinformatics, 2009
- Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population DynamicsMolecular Biology and Evolution, 2008
- Evolutionary trees from DNA sequences: A maximum likelihood approachJournal of Molecular Evolution, 1981
- A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequencesJournal of Molecular Evolution, 1980