Phylogenetics: BEAST Lab

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Adiantum.png EEB 349: Phylogenetics
In this lab you will learn how to use the program BEAST, and its companion BEAUTi, written by Alexei Drummond and Andrew Rambaut. BEAST differs from MrBayes in that it is designed to jointly infer rooted trees and divergence times under a relaxed clock model, the argument being that if it is possible to infer divergence times calibrated by constraints on the ages of certain groups, then this information should also be important for getting the tree topology correct.

You will (part 1) go through a practical designed by BEAST's authors, then (part 2) you will analyze a data set you simulate yourself to confirm that the program works as expected (and, more importantly, you understand how to set it up to work as expected).

Download BEAST and the practical

Download the appropriate version of BEAST 1.8.0 from the BEAST web site. The BEAST web site will direct you to the BEAST google code website, which is where the software distributions are actually hosted. While you are on the google code site, also download the practical titled Divergence Dating (Primates) I will assume you already have FigTree and Tracer installed. If not, install these two programs as well from the BEAST web site.

BEAST and BEAUti form a pair. BEAUti is a user-friendly, graphical Java application that can be used to create the data file that is then fed to BEAST, which is neither user-friendly nor graphical, but is nevertheless also written in Java. Thus, to do anything with BEAST, you will need a working Java runtime environment. You will actually use the cluster to run BEAST, but you will need to run BEAUti on your own laptop. If you have trouble getting Java running on your laptop, pair with another student until you have an XML file. At that point, you can use your own computer to interact with the cluster.

Work through the practical

Unzip the practical and work through it.