BEAST 2 is a new open-source, extensible, and flexible software platform for Bayesian evolutionary analysis. It is a re-design of the popular BEAST 1 platform to address structural deficiencies that became evident as BEAST 1 evolved. A key deficiency 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. BEAST 2 provides the same core Bayesian evolutionary analyses that have made BEAST 1.x popular. It implements relaxed clocks, non-parametric coalescent analysis, multispecies coalescent inference, phylogeography, and others. BEAUti 2 has been designed from the ground up to be seamlessly integrated with the BEAST analysis engine so that all the models developed can easily be added to the user interface without any GUI programming. In addition, BEAST 2 has a sequence simulator for simulation studies, post-processing tools (such as LogAnalyzer, LogCombiner, DensiTree), and comprehensive documentation for both users and developers. The advantages of BEAST 2 include the ability to check-point and resume analyses, reload analysis specification in BEAUTi, package architecture including extensible XML format and template-based GUI development, and include details of model in trace files. BEAST 2 is well documented, and the documentation is accessible through the BEAST2 wiki at http://beast2.org. It contains general information about the programs in the BEAST distribution, frequently asked questions, and a number of tutorials that provide step-by-step instructions on performing various kinds of analysis, including divergence dating, measurable evolving populations, STAR-BEAST, and phylogeography. Furthermore, there is a mailing list for users and developers and a reference book available (http://beast2.org/book.html) and is expected to be published in 2014. BEAST 2 includes several new evolutionary models, such as the spike-and-slab mixture model, the birth-deathBEAST 2 is a new open-source, extensible, and flexible software platform for Bayesian evolutionary analysis. It is a re-design of the popular BEAST 1 platform to address structural deficiencies that became evident as BEAST 1 evolved. A key deficiency 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. BEAST 2 provides the same core Bayesian evolutionary analyses that have made BEAST 1.x popular. It implements relaxed clocks, non-parametric coalescent analysis, multispecies coalescent inference, phylogeography, and others. BEAUti 2 has been designed from the ground up to be seamlessly integrated with the BEAST analysis engine so that all the models developed can easily be added to the user interface without any GUI programming. In addition, BEAST 2 has a sequence simulator for simulation studies, post-processing tools (such as LogAnalyzer, LogCombiner, DensiTree), and comprehensive documentation for both users and developers. The advantages of BEAST 2 include the ability to check-point and resume analyses, reload analysis specification in BEAUTi, package architecture including extensible XML format and template-based GUI development, and include details of model in trace files. BEAST 2 is well documented, and the documentation is accessible through the BEAST2 wiki at http://beast2.org. It contains general information about the programs in the BEAST distribution, frequently asked questions, and a number of tutorials that provide step-by-step instructions on performing various kinds of analysis, including divergence dating, measurable evolving populations, STAR-BEAST, and phylogeography. Furthermore, there is a mailing list for users and developers and a reference book available (http://beast2.org/book.html) and is expected to be published in 2014. BEAST 2 includes several new evolutionary models, such as the spike-and-slab mixture model, the birth-death