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PLoS Comput Biol. 2014 Apr 10;10(4):e1003537. doi: 10.1371/journal.pcbi.1003537. eCollection 2014 Apr.

BEAST 2: a software platform for Bayesian evolutionary analysis.

Author information

1
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
2
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
3
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.
4
Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, United States of America; Department of Biostatistics, School of Public Health, University of California, Los Angeles, Los Angeles, California, United States of America.
5
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
6
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand.

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.

PMID:
24722319
PMCID:
PMC3985171
DOI:
10.1371/journal.pcbi.1003537
[Indexed for MEDLINE]
Free PMC Article

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