BEAST 2: a software platform for Bayesian evolutionary analysis

PLoS Computational Biology
Remco R BouckaertAlexei J Drummond

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 ...Continue Reading

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Feb 26, 2019·The Journal of Infectious Diseases·Tetyana I VasylyevaNuno R Faria
Mar 30, 2019·The New Phytologist·Bryan T Piatkowski, A Jonathan Shaw
Mar 17, 2019·American Journal of Epidemiology·Joseph A Lewnard, Arthur L Reingold
Jun 15, 2016·Scientific Reports·Ranko GacesaPaul F Long
May 5, 2018·Nature Communications·Evan P EconomoBenoit Guénard
Feb 21, 2019·International Journal of Systematic and Evolutionary Microbiology·Ofir LidorEinat Zchori-Fein
Apr 25, 2019·Evolution; International Journal of Organic Evolution·Victoria CulshawIsabel Sanmartín
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May 8, 2019·Nature Plants·Hong-Tao LiDe-Zhu Li
May 8, 2019·Proceedings of the National Academy of Sciences of the United States of America·Laurent SagartJohann-Mattis List
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May 21, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Jonathan A PolonskyThibaut Jombart
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