Phylogenetics: BEAST Lab
|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 version of BEAST 2.4.0 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.
Analysis of simulated data
Download the file simyule.nex to your hard drive and import it into BEAUTi using the File > Import alignment menu command. An entry called simyule should appear in the Partitions section.
The tree from which these data were simulated was itself simulated using the Yule model. Here are some facts about the true tree:
|Number of leaves (species)||20|
|Per-lineage speciation rate||10|
|Tree length (sum of all edge times)||1.77537|
|Tree height (length of path from root to any tip)||0.279743|
Sequence data (10000 sites) was simulated using this Yule tree. Here are some facts about the true substitution model:
|Gamma rate heterogeneity shape||0.5|
|Equilibrium frequency for A||0.3|
|Equilibrium frequency for C||0.2|
|Equilibrium frequency for G||0.2|
|Equilibrium frequency for T||0.3|
|Kappa (trs./trv. rate ratio)||4.0|