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  • We present a new open source, extensible and flexible software platform for Bayesian evolutionary analysis called BEAST 2. 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. The first generation Bayesian Evolutionary Analysis by Sampling Trees (BEAST) package [1], [2] has become a popular platform for solving such problems and takes a modeling philosophy that all of these evolutionary analysis problems share at their core one or more phylogenetic time-trees. This paper describes the overarching design and implementation details of a re-write of the BEAST platform that we have designated BEAST 2, as well as presenting examples of some significant new models developed especially for this new platform. The BEAST 2 platform is an open source project and is anonymously available on a source repository hosted by GitHub at https://github.com/CompEvol/beast2 and supplementary material Code S1. This example file runs on BEAST 2.1.0 with the MultiTypeTree package (http://compevol.github.io/MultiTypeTree/).
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