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).

Contents

Part 1: Primate practical

Download BEAST and the practical

Download the appropriate version of BEAST 1.6.1 (or later) from the BEAST web site. While there, also download the practical titled Divergence Dating (Primates) v1.1a.zip. I will assume you already have Tracer and FigTree installed. If not, install these two programs as well.

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 also written in Java. Thus, to do anything with BEAST, you will need a working Java runtime environment.

Work through the practical

Unzip the practical and work through it. This will probably take the entire lab period. That's fine and will give me time to create Part 2 before next week.

Part 2: Analysis of simulated data

TODO: hopefully will be ready by next week's lab

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