Programme

This is only a preliminary programme and the titles of talks and contents of tutorial sessions are subject to change.

Monday
2017/07/24
Tuesday
2017/07/25
Wednesday
2017/07/26
Thursday
2017/07/27
Friday
2017/07/28
08:15 Welcome and organisation Announcements Announcements Announcements Announcements
08:30 Introduction of instructors and participants Alexei Drummond:
Tree priors, clocks and skylines
Tim Vaughan:
Modelling structured populations
Huw Ogilvie
Multi-species coalescent inference
Tanja Stadler:
Modelling birth-death processes
Erik Volz:
Pathogen source attribution
Nuno Faria:
Real-time phylodynamics
10:30 Coffee break Coffee break Coffee break Coffee break Coffee break
11:00 Oliver Pybus:
Basic principles of statistical inference
Louis du Plessis:
Bayesian phylogenetics in BEAST 2
Louis du Plessis:
Model averaging, selection and adequacy
Tutorial 2a:
Substitution model averaging
Nicola Müller:
Structured coalescent approximations
Tutorial 3a:
Phylogeography in BEAST2 with MASCOT
BEAST Clinic:
Personal projects
and troubleshooting
Nicola de Maio:
Transmission tree reconstruction
Tutorial 5a:
Transmission tree inference in BEAST2 with SCOTTI
13:00 Lunch Lunch Lunch Lunch Lunch
14:00 Oliver Pybus:
Introduction to infectious disease phylodynamics
Tutorial 1a:
Relaxed phylogenetics in BEAST 2
Stéphane Hué:
Troubleshooting the BEAST
Tutorial 2b and 2c:
Skyline plots and
Troubleshooting
Tutorial 3b and 3c:
Species trees with StarBEAST2 and calibrated species trees
Joëlle Barido-Sottani:
The fossilized birth-death
process

Tutorial 4b:
Dating species divergences with the fossilized birth-death process
Tim Vaughan:
Inferring bacterial recombination graphs
Tutorial 5b:
Bacterial phylogenetics in BEAST 2 with BACTER
16:00 Afternoon tea Afternoon tea Free time for excursions Afternoon tea Afternoon tea
16:30 Stéphane Hué:
Setting priors and initial values
Tutorial 1b:
Prior selection and clock calibration
BEAST Clinic:
Personal projects and troubleshooting
Jūlija Pečerska:
Advanced birth-death models

Tutorial 4a:
Population structure using the multitype birth-death model

General discussion and closure

Departure at 17:00
19:00 Dinner in Indian curry house London walking tour Pub dinner

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.

  • 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 v2.4.7 for the workshop (download).
  • FigTree: FigTree is a graphical viewer of phylogenetic trees, specificly designed to display summarized 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).
  • Java 8 JDK: This Java SE Developlment Kit is required for BEAST 2 (download).
  • RStudio (optional): RStudio IDE is a user interface for R (download).
  • Python: Python scripts will be used in one of the tutorials. Python should already be installed if you're using Mac OS X or Linux. For one of the scripts the Python package graphviz or graph-tool is required.

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.

We are aware that most of the books on this list are quite expensive and may not be available in your institution's library. However, with a moderate amount of Googling you can get your hands on preprints or older versions of some of these books. (There is also currently a 20% discount available for Ziheng Yang's book...)