Lab #9: Taming the BEAST

Divergence Time Estimation using BEAST 2

Introduction

BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using various 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. A core aspect of the BEAST 2 design philosophy is to allow researchers to extend the core program without the involvement of the BEAST 2 developers. New methods are implemented as standalone packages that are developed and maintained separately of BEAST 2 itself.

The tutorial we will follow today covers only a small part of BEAST’s abilities. However, there is a great resource, Taming the BEAST that contains a comprehensive set of BEAST 2 tutorials in one location that can be used to learn more about the program.

The program has been originally described in PloS Comp. Biol. article. A recent book “Bayesian Evolutionary Analysis with BEAST” covers theory behind the analysis in addition to the program itself.

Getting Started

Software

BEAST 2 package is available for Mac, Windows, and Linux. It contains both the BEAUti and the BEAST programs that we will use for this exercise. We will also use TreeAnnotator and DensiTree, wich are distributed in the same package.

In addition, we will use Tracer and FigTree, both of which have executables for Windows and Macs.

Because several of these programs use GUI, we’ll use them on our personal computers.

Install these programs on your computer and let me know if there are any problems!

Tutorial

We will be using the Introduction to BEAST2 tutorial from the [Taming the BEAST] website. This is a “simple” introductory tutorial to help you get started with the program.

Dr. Tracy Heath from our department has contributed another great tutorial Dating Species Divergences with the Fossilized Birth-Death process, which contains a lot of insightful background information. You can try it in your spare time!

The data for the tutorial is available here and also in the lab9/data directory in the GitHub repository for the class.

Good Luck!

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