BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis

Abstract

Elaboration of Bayesian phylogenetic inference methods has continued at pace in recent years with major new advances in nearly all aspects of the joint modelling of evolutionary data. It is increasingly appreciated that some evolutionary questions can only be adequately answered by combining evidence from multiple independent sources of data, including genome sequences, sampling dates, phenotypic data, radiocarbon dates, fossil occurrences, and biogeographic range information among others. Including all relevant data into a single joint model is very challenging both conceptually and computationally. Advanced computational software packages that allow robust development of compatible (sub-)models which can be composed into a full model hierarchy have played a key role in these developments. Developing such software frameworks is increasingly a major scientific activity in its own right, and comes with specific challenges, from practical software design, development and engineering challenges to statistical and conceptual modelling challenges. BEAST 2 is one such computational software platform, and was first announced over 4 years ago. Here we describe a series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release.

Keywords

Affiliated Institutions

• University of Gothenburg SE
• University of Technology Sydney AU
• European Bioinformatics Institute GB
• SIB Swiss Institute of Bioinformatics CH
• Chinese Academy of Sciences CN
• The University of Melbourne AU
• University of California, Los Angeles US
• Institute of Vertebrate Paleontology and Paleoanthropology CN
• North Carolina State University US
• ETH Zurich CH
• Max Planck Institute for the Science of Human History DE
• Imperial College London GB
• University of Otago NZ
• University of Auckland NZ
• University of Basel CH
• Rice University US
• University of Oxford GB
• University of Edinburgh GB

Related Publications