BEAST2 (http://www.beast2.org) is a free software package for Bayesian evolutionary analysis of molecular sequences using MCMC and strictly oriented toward inference using rooted, time-measured phylogenetic trees.

It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results.

In this simple tutorial you will get acquainted with the basic workflow of BEAST2 and the software tools most commonly used to interpret the results of analyses. Bear in mind that this tutorial is designed only to help you get started using BEAST2. This tutorial does not discuss all the choices and concepts in detail, as they are discussed in further tutorials. Interspersed throughout the tutorial are topics for discussion. These discussion topics are optional, however if you work through them you will have a better understanding of the concepts discussed in this tutorial. Feel free to skip the discussion topics and come back to them later, while running the analysis file, or after finishing the whole tutorial.