BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

TLDR

BEAST 2 is a redesign of the popular BEAST 1 platform to address structural deficiencies, notably the lack of post‑deployment extensibility, that emerged as BEAST 1 evolved. The authors introduce BEAST 2, an open‑source, extensible platform for Bayesian evolutionary analysis. BEAST 2 implements a package‑management system and a redesigned architecture that allows third‑party extensions, shared MCMC state, and seamless integration between the analysis engine and the user interface. The platform’s package architecture supports new models (e.g., birth‑death‑sampling tree priors, phylodynamics, model averaging, site partitioning) and enables checkpointing, multi‑processor support, and easy UI integration through XML templates.

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.