BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

April 2014 | Volume 10 | Issue 4 | e1003537 | Remco Bouckaert, Joseph Heled, Denise Kühnert, Tim Vaughan, Chieh-Hsi Wu, Dong Xie, Marc A. Suchard, Andrew Rambaut, Alexei J. Drummond
The paper introduces BEAST 2, an open-source, extensible, and flexible software platform for Bayesian evolutionary analysis. BEAST 2 is a redesign of the popular BEAST 1 platform to address structural deficiencies, particularly the lack of post-deployment extensibility. Key improvements include a fully developed package management system that allows third-party developers to add new functionalities without requiring a new software release. This system supports the integration of various models, such as birth-death-sampling tree priors, phylodynamics, and model averaging for substitution models and site partitioning. Additionally, BEAST 2 introduces the ability to read and write the entire state of the MCMC chain to/from disk, facilitating checkpointing and multi-processor computing. The user interface, BEAUti 2, has been re-designed to integrate seamlessly with the analysis engine, allowing for easy addition of new functionalities through a simple XML template-based mechanism. The paper also highlights several new evolutionary models implemented in BEAST 2, including a spike-and-slab mixture model for nucleotide substitution models, the birth-death skyline model, and the structured coalescent model. The platform is available as open-source software on GitHub and through a dedicated website, encouraging contributions from the research community.The paper introduces BEAST 2, an open-source, extensible, and flexible software platform for Bayesian evolutionary analysis. BEAST 2 is a redesign of the popular BEAST 1 platform to address structural deficiencies, particularly the lack of post-deployment extensibility. Key improvements include a fully developed package management system that allows third-party developers to add new functionalities without requiring a new software release. This system supports the integration of various models, such as birth-death-sampling tree priors, phylodynamics, and model averaging for substitution models and site partitioning. Additionally, BEAST 2 introduces the ability to read and write the entire state of the MCMC chain to/from disk, facilitating checkpointing and multi-processor computing. The user interface, BEAUti 2, has been re-designed to integrate seamlessly with the analysis engine, allowing for easy addition of new functionalities through a simple XML template-based mechanism. The paper also highlights several new evolutionary models implemented in BEAST 2, including a spike-and-slab mixture model for nucleotide substitution models, the birth-death skyline model, and the structured coalescent model. The platform is available as open-source software on GitHub and through a dedicated website, encouraging contributions from the research community.
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