Phylogenetics: BEAST Lab

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Adiantum.png EEB 5349: Phylogenetics
In this lab you will learn how to use the program BEAST, and its companion BEAUTi, written by Alexei Drummond, Andrew Rambaut, Marc Suchard, Remco Bouckaert, and numerous other contributors. BEAST specializes in estimating divergence times under uncorrelated relaxed clock models, estimating species trees using a model that accounts for the independent coalescent history of each gene tree, and Bayesian skyline analyses that estimate population growth or decline through time. While BEAST itself is written in C and Java and has no user interface, the companion program BEAUTi has a nice graphical user interface that allows you to create an XML data file that is consulted by BEAST when it runs.

In this lab, you will use BEAST to estimate divergence times. Rather than analyze a real data set, you will simulated a data set in which you know the true values of all parameters, and then see how to obtain estimates of those parameters in BEAST.

Login to the UConn Bioinformatics cluster

Once you login, type


to obtain a session on a currently unused node.

Download BEAUTi and BEAST

While we will be using BEAST on the cluster, you will need to download the software locally in order to get BEAUTi, which cannot be easily run remotely on the cluster because of its interactive GUI (Graphical User Interface).

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.