Workshop on Population and Speciation Genomics

Český Krumlov, 2018

This page contains teaching materials to support BEAST 2 practical sessions at the Workshop on Molecular Evolution in Český Krumlov, 2018.

Required Software

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

• Java version 8 JDK. (Not version 9.)
• BEAST 2.4.8
• Tracer 1.6
• FigTree 1.4.3
• R (recent version)
• 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] [pre-generated logs]
   • Approximate structured coalescent inference using MASCOT [html] [pre-generated logs]
3. Species delimitation with SNAPP [zip]
4. Species network inference tutorial [zip] [pre-generated logs]

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 taming-the-beast.org/tutorials.

Further documentation

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