Workshop Programme

Where possible, links have been added from the programme below to the corresponding tutorials and lecture slides. Additional links will be added as they become available.

09:00 Alexei Drummond
Bayesian Phylogenetics and BEAST
Remco Bouckaert
Phylogenetic model selection and averaging
Tim Vaughan, Jana Huisman, Nicola Müller
Bayesian Phylodynamics: Skylines, Fossilization and Structure
Mike Lee
Bayesian phylogenetics for phenotypic and palaeontological datasets (part 1, part 2)
Sebastián Duchêne
Tip-dating and phylodynamics
11:00 Morning Tea Morning Tea Morning Tea Morning Tea Morning Tea
11:30 Tim Vaughan
First Steps in BEAST 2
(lecture, tutorial)
Remco Bouckaert
Substitution model averaging
Mike Lee
Arid biomes as a source, not sink, for Australian lizard biodiversity
(public lecture)
Jana Huisman
Fossilized birth-death model analyses
Nicola Müller
Isolation with Migration using Coupled MCMC
12:30 Free afternoon
(packed lunch provided)
13:00 Lunch Lunch Lunch Lunch
14:00 Jana Huisman
Prior Selection & Troubleshooting
(lecture, tutorial)
Simon Ho
Molecular Dating (lecture)
David Duchêne
Species trees and gene trees (lecture)
Tim Vaughan
Bacterial genomics
(lecture, tutorial)
15:00 Jérémie Sciré, Nicola Müller
Analyzing structured populations under birth-death and coalescent models
(tutorial 1, tutorial 2)
15:30 Afternoon Tea Afternoon Tea Afternoon Tea
16:00 Welcome and registration
(Courtyard Cafe,
University of Sydney)
Nicola Müller
Skyline Plot Tutorial
(lecture, tutorial)
Cara Van Der Wal, Daej Arab, Yi-Kai Tea
Divergence time estimation
18:00 Buffet dinner cruise
(Sydney Harbour, Depart from King St Wharf)
18:30 Dinner
(Thai Pothong, Newtown)

Required Software

You are required to bring your own laptop to the workshop. Power strips are available for each participant to keep their devices charged during the workshop. The software below must be installed prior to arrival.

  • Java 8 or higher: This is required by BEAST 2 (download).
  • BEAST 2: BEAST 2 is 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 v2.5.2 for the workshop (download).
  • FigTree: FigTree is a graphical viewer of phylogenetic trees, specifically designed to display summarised and annotated trees produced by BEAST (download).
  • Tracer: Tracer is a program for analysing the trace files generated by Bayesian MCMC runs. It can be used to check mixing, ESS, parameter correlations, etc. (download).
  • BEAGLE (optional): BEAGLE is a high-performance library that can perform the core calculations in BEAST2 (and many other phylogenetics packages) much faster. BEAGLE isn’t necessary for the workshop, but it will speed up your analyses (download).
  • R: R is a free software environment that provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering) and graphical techniques, and is highly extensible (download).
  • RStudio (optional): RStudio provides a friendly front-end for R (download).

Pre-workshop recommended reading

Statistics and mathematics primers

We are aware that some of the workshop participants do not have a mathematical background and may have difficulty understanding some of the theory. The two links below can help to refresh the basic concepts, but are by no means meant to be comprehensive resources.

  • Seeing Theory: This website gives a very brief, but pretty and easy to understand introduction to many of the fundamental concepts in statistics.
  • Ziheng Yang’s statistics primer: Gives a more in-depth introduction to the topic.

Phylogenetics and phylodynamics books

The books below are not all focused on BEAST or even Bayesian phylogenetics. However, each of the books contains at least one background chapter on the theory of molecular evolution, as well as more in-depth chapters on the models implemented in BEAST and BEAST 2. Most of the books also contain at least some discussion of Bayesian inference.

In addition, the following review papers might be useful: