Name
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. |
Year | DOI | Venue |
|---|---|---|
2014 | 10.1371/journal.pcbi.1003537 | PLOS COMPUTATIONAL BIOLOGY |
Keywords | Field | DocType |
programming languages,bayes theorem | Software release life cycle,Architecture,XML,Computer science,Software,Bioinformatics,User interface,Extensibility,Software development,Bayesian probability | Journal |
Volume | Issue | ISSN |
10 | 4 | 1553-734X |
Citations | PageRank | References |
23 | 1.62 | 4 |
Authors | ||
9 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Remco R. Bouckaert | 1 | 484 | 82.93 |
| Joseph Heled | 2 | 23 | 1.95 |
| Denise Kühnert | 3 | 25 | 2.71 |
| Tim Vaughan | 4 | 23 | 1.62 |
| Chieh-Hsi Wu | 5 | 25 | 2.36 |
| Dong Xie | 6 | 23 | 1.62 |
| Marc A Suchard | 7 | 213 | 27.83 |
| Andrew Rambaut | 8 | 446 | 81.92 |
| Alexei Drummond | 9 | 130 | 14.06 |