Introduction

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.

Publications

  1. BEAST 2: a software platform for Bayesian evolutionary analysis.
    Cite this
    Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ, 2014-04-01 - PLoS computational biology
  2. Bayesian phylogenetics with BEAUti and the BEAST 1.7.
    Cite this
    Drummond AJ, Suchard MA, Xie D, Rambaut A, 2012-08-01 - Molecular biology and evolution
  3. BEAST: Bayesian evolutionary analysis by sampling trees.
    Cite this
    Drummond AJ, Rambaut A, 2007-11-01 - BMC evolutionary biology

Credits

  1. Remco Bouckaert
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  2. Joseph Heled
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  3. Denise Kühnert
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  4. Tim Vaughan
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  5. Chieh-Hsi Wu
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  6. Dong Xie
    Developer

    Computational Evolution Group, Department of Computer Science, New Zealand

  7. Marc A Suchard
    Developer

    Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, United States of America

  8. Andrew Rambaut
    Developer

    Institute of Evolutionary Biology, University of Edinburgh, United Kingdom of Great Britain and Northern Ireland

  9. Alexei J Drummond
    Investigator

    Computational Evolution Group, Department of Computer Science, New Zealand

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Summary
AccessionBT007043
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionNew Zealand
Submitted ByAlexei J Drummond