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BEAST 2: a software platform for Bayesian evolutionary analysis

Bouckaert, Remco ; Heled, Joseph ; Kühnert, Denise ; Vaughan, Tim ; Wu, Chieh-Hsi ; Xie, Dong ; Suchard, Marc A ; Rambaut, Andrew ; Drummond, Alexei J Prlic, Andreas

PLoS computational biology, 2014-04, Vol.10 (4), p.e1003537 [Periódico revisado por pares]

United States: Public Library of Science

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  • Título:
    BEAST 2: a software platform for Bayesian evolutionary analysis
  • Autor: Bouckaert, Remco ; Heled, Joseph ; Kühnert, Denise ; Vaughan, Tim ; Wu, Chieh-Hsi ; Xie, Dong ; Suchard, Marc A ; Rambaut, Andrew ; Drummond, Alexei J
  • Prlic, Andreas
  • Assuntos: Bayes Theorem ; Bayesian statistical decision theory ; Biological Evolution ; Biology and Life Sciences ; Computational biology ; Evolution ; Phylogenetics ; Programming Languages ; Software ; Technology application ; Trees
  • É parte de: PLoS computational biology, 2014-04, Vol.10 (4), p.e1003537
  • Notas: Analyzed the data: DK TV CHW. Wrote the paper: RB JH DK TV CHW MAS AR AJD. Developed software: RB JH DK TV CHW DX MAS AR AJD.
    The authors have declared that no competing interests exist.
  • Descrição: 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.
  • Editor: United States: Public Library of Science
  • Idioma: Inglês
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