Workshop Programme

09:00 Alexei Drummond
Introduction to Bayesian Phylogenetics (part 1)
Sebastián Duchêne
Clock models, site models, model comparison
Tanja Stadler
Birth-death models
Alexandra Gavryushkina
Modelling Fossilization
Nicola Müller
Multi-species models
Tim Vaughan
Modelling recombination
10:45 Morning Tea Morning Tea Morning Tea Morning Tea Morning Tea
11:15 Louis Du Plessis
First Steps in BEAST
(lecture, tutorial)
Carsten Magnus
Model Averaging and bModelTest
(lecture, tutorial)
Tim Vaughan
Bayesian Skyline Plot and Birth-death Skyline Tutorial
Jérémie Sciré
Structured Birth-death Tutorial
Tim Vaughan
Bacter tutorial
12:45 Lunch Lunch Lunch Lunch Lunch
14:00 Vladimir Minin
Introduction to Bayesian Phylogenetics (part 2)
Nicola Müller
The Structured Coalescent
Nicola Müller
MASCOT Tutorial
Activities (e.g. Hiking, swimming, etc.) Rachel Warnock
FBD Model Tutorial
Nicola Müller
StarBEAST2 Tutorial
15:45 Afternoon Tea Afternoon Tea Afternoon Tea Afternoon Tea
16:15 Veronika Boskova
Setting Priors
Jūlija Pečerska
Tim Vaughan
Understanding BEAST 2 XML
BEAST Clinic
16:45 Welcome Apero Veronika Boskova
Setting Priors Tutorial
Jūlija Pečerska
Trouble-shooting Tutorial
Tim Vaughan
XML Hacking Tutorial
19:00 Dinner Dinner Dinner Dinner Dinner
20:00 Introduction of Participants BEAST Clinic (informal) BEAST Clinic (informal) BEAST Clinic (informal) BEAST Clinic (informal)

Lecture slides

Slides to lectures are available from here

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 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: