BEAST 2: a software platform for Bayesian evolutionary analysis.
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.
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
Remco
R
Bouckaert
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
Joseph
J
Heled
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand; Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
Denise
D
Kühnert
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.
Tim
T
Vaughan
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
Chieh-Hsi
CH
Wu
Computational Evolution Group, Department of Computer Science, University of Auckland, Auckland, New Zealand.
Dong
D
Xie
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.
Marc A
MA
Suchard
Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom.
Andrew
A
Rambaut
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.
Alexei J
AJ
Drummond
D001499:Bayes Theorem; D005075:Biological Evolution; D011381:Programming Languages; D012984:Software