BEAST 2 workshop

The final workshop in the Biosystematics 2023 conference's workshop series will be on BEAST 2, an open-source software package for Bayesian phylogenetic analyses of molecular sequences.

The aim of this one-day workshop is to equip participants with the skills and core knowledge to confidently perform phylogenetic analyses of their own. It is open to graduate students and scientists interested in the analysis of genomic data and molecular evolution.

The workshop will consist of lectures and hands-on tutorials with a focus on dating and species delimitation presented by Dr Remco Bouckaert, main architect of BEAST 2, and Dr Jordan Douglas, expert developer of many methods in BEAST 2.

Registration is via the conference webage. You are welcome to register for the workshop without attending the conference. Registrations close 4 November.*

* Conference registration has now closed but there are some few workshop places available. Please contact Claire Stephens directly via email if you would like to attend.

Participants will need to bring their own laptops with the following software installed

  • BEAST 2: a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. We will be using this software to perform analyses on the data brought to the workshop. We will be using BEAST v2.7 for the workshop.
  • FigTree: a graphical viewer of phylogenetic trees, specifically designed to display summarised and annotated trees produced by BEAST.
  • Tracer: a program for analysing the trace files generated by Bayesian MCMC runs. It can be used to check mixing, ESS, parameter correlations, etc.
  • Java 8 or higher: You may need to install a Java JDK to run FigTree and Tracer.

Pre-workshop recommended reading

Some background probability and statistics knowledge will be needed to follow the theory in the workshop. This site can help to refresh the basic concepts. Ziheng Yang’s statistics primer provides a more in-depth introduction to the topic.

Alexei Drummond's and Remco Bouckaert's book Bayesian Evolutionary Analysis with BEAST has background chapters on the theory of molecular evolution, as well as more in-depth chapters on the models implemented in BEAST 2.

Topics

  1. Introduction to Bayesian phylogenetics
  2. Multispecies coalescent
  3. Model testing

There will be three 1hr lectures, three 1hr tutorials, and food breaks. The links to the tutorials can be found here.

Schedule

  • 9.00 Lecture: Introducing Bayesian phylogenetics
  • 10.00 Tutorial: Introduction to BEAST2
  • 10.30 Tea break
  • 11.00 Continue tutorial
  • 11.30 Lecture: Multi species coalescent
  • 12.30 Lunch
  • 13.30 Tutorial: Starbeast3
  • 14.30 Lecture: Asking & answering questions with Bayesian phylogenetics
  • 15.00 Tea break
  • 15.30 Continue lecture
  • 16.00 Tutorial: Species delimitation
  • 17.00 Wrap up

Venue

The workshop will be held in the Slatyer Seminar Room, 2nd floor RN Robertson Building at ANU (up the ramp from the front foyer, above the Little Pickle cafe). Light refreshments for tea/coffee and lunch breaks will be provided.

BEAST 2 clinic

During the conference, Remco and Jordan will host a `BEAST clinic' where you can consult on all your BEAST 2 questions, issues and requests. At the clinic, they will help you out with any problems setting up an analysis, interpreting the results or understanding what is going on. The clinic will be open during all coffee breaks.