Dataset Information

BEAST 2: a software platform for Bayesian evolutionary analysis.

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.

SUBMITTER: Bouckaert R

PROVIDER: S-EPMC3985171 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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BEAST 2: a software platform for Bayesian evolutionary analysis.

Bouckaert Remco R Heled Joseph J Kühnert Denise D Vaughan Tim T Wu Chieh-Hsi CH Xie Dong D Suchard Marc A MA Rambaut Andrew A Drummond Alexei J AJ

PLoS computational biology 20140410 4

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 di ...[more]

PMID: 24722319

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Dataset Information

BEAST 2: a software platform for Bayesian evolutionary analysis.

Publications

BEAST 2: a software platform for Bayesian evolutionary analysis.

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