TY - JOUR T1 - BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis JF - bioRxiv DO - 10.1101/474296 SP - 474296 AU - Remco Bouckaert AU - Timothy G. Vaughan AU - Joëlle Barido-Sottani AU - Sebastián Duchêne AU - Mathieu Fourment AU - Alexandra Gavryushkina AU - Joseph Heled AU - Graham Jones AU - Denise Kühnert AU - Nicola De Maio AU - Michael Matschiner AU - Fábio K. Mendes AU - Nicola F. Müller AU - Huw Ogilvie AU - Louis du Plessis AU - Alex Popinga AU - Andrew Rambaut AU - David Rasmussen AU - Igor Siveroni AU - Marc A. Suchard AU - Chieh-Hsi Wu AU - Dong Xie AU - Chi Zhang AU - Tanja Stadler AU - Alexei J. Drummond Y1 - 2018/01/01 UR - http://biorxiv.org/content/early/2018/11/19/474296.abstract N2 - 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.Author summary Bayesian phylogenetic inference methods have undergone considerable development in recent years, and joint modelling of rich evolutionary data, including genomes, phenotypes and fossil occurrences is increasingly common. 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 scientific software is increasingly crucial to advancement in many fields of biology. The challenges range from practical software development and engineering, distributed team coordination, conceptual development and statistical modelling, to validation and testing. BEAST 2 is one such computational software platform for phylogenetics, population genetics and phylodynamics, and was first announced over 4 years ago. Here we describe the full range of new tools and models available on the BEAST 2.5 platform, which expand joint evolutionary inference in many new directions, especially for joint inference over multiple data types, non-tree models and complex phylodynamics. ER -