An introduction to BEAST and its friends

BEAST is a free (as in freedom) software package that uses MCMC to perform Bayesian phylogenetic inference.

Project website: beast2.org

• Download software
• Documentation and FAQs
• Tutorials
• ...

What is the relationship between BEAST 2 and BEAST 1?

• BEAST 2 is a complete rewrite of BEAST 1.
• Many of the same authors were involved.
• Development still continues on BEAST 1.x
• The number of models included in BEAST 2 is quickly exceeding the number for BEAST 1.
• Here, whenever I say BEAST I'm referring to BEAST 2.

BEAST components

• BEAST2: Software implementing MCMC for model parameter and tree inference
• BEAUti: GUI for setting up the input file
• Tracer: Tool for summarizing parameter posteriors
• Tree Annotator: Tool for summarizing tree posteriors
• Figtree: Tool for visualising trees

BEAST Workflow

What is a BEAST Package?

• Much of BEAST's functionality is contained in modular packages.
• Models can be implemented by groups not affiliated with the BEAST development team.
• In order to run analyses using these models, the relevant packages must be installed.

What is BEAUti?

• BEAUti is a Backronym:
  Bayesian Evolutionary Analysis Utility
• A GUI front-end for BEAST that assists in constructing the XML files that describe BEAST analyses.
• The usual way that many BEAST analyses are set up.

A couple of points:

• XML files generated by BEAUti can be loaded back into BEAUti.
• Packages containing models used by analysis must be installed before the XML is loaded.