Workshop on Population and Speciation Genomics

Český Krumlov, 2016

This page contains teaching materials to support BEAST 2 practical sessions at the Workshop on Molecular Evolution in Český Krumlov, 2016.

Required Software

The following software must be installed on your computer to complete these tutorials:

• Java version 8
• BEAST 2.3.3 (pre-release 3)
• Tracer 1.6
• FigTree 1.4.2
• R
• An up-to-date version Firefox or Chrome
• BEAGLE (optional)

Tutorials

The following tutorials will be taught during practical sessions in the Workshop.

1. Extended Bayesian Skyline Plot (EBSP) tutorial [zip] [logs for a 100M run]
2. Sructured Coalescent tutorials
   • Full structured coalescent inference using MultiTypeTree [html] [xml and logs]
   • Approximate structured coalescent inference using BASTA [html] [xml and logs]
3. Bayes Factor Delimitation of Species (BFD*) [zip]

Extras

• How to manage packages.
• An extra set of tutorials that you may find useful to investigate in your own time can be found at www.beast2.org/tutorials.

Further documentation

Further documentation on BEAST2 can be found on the BEAST2 website.

If you are having trouble starting BEAST and BEAUti by double-clicking on Windows it is probably because you have more than one Java version installed. Make sure “java — version” reports version 1.8 and then follow these instructions to start BEAUti and BEAST from the Command Prompt.