Taming the BEAST 2020

Zentrum Ländli, Oberägeri, Switzerland
Cancelled

This workshop has been CANCELLED due to the COVID-19 pandemic.

Workshop Programme

Important: this is a draft programme only and may be subject to change.

Sunday Monday Tuesday Wednesday Thursday Friday
09:00 Alexei Drummond
Introduction to Bayesian Phylogenetics 		Tanja Stadler
Birth-death models and macroevolution 		Remco Bouckaert
Language evolution and phylogeography 		Denise Kühnert
Modelling epidemics with BEAST 2 		Louis du Plessis
Real-time outbreak analysis
Tim Vaughan
Multi-species models
10:45 Morning Tea Morning Tea Morning Tea Morning Tea Morning Tea
11:15 First Steps in BEAST
(lecture, tutorial) 		Fossilized Birth Death Model
(tutorial) 		Language evolution
(tutorial) 		Structured Birth-death Model
(tutorial) 		StarBEAST 2
(tutorial)
12:45 Lunch Lunch Lunch Lunch Lunch
14:00 Substitution models
(tutorial) 		Bayesian Skyline Plot and Birth-death Skyline Plot
(tutorial) 		Activities (e.g. Hiking, swimming, etc.) The Structured Coalescent
(lecture, tutorial) 		Inferring recombination graphs with BEAST 2
(lecture, tutorial)
15:45 Afternoon Tea Afternoon Tea Afternoon Tea Afternoon Tea
16:15 Setting Priors
(lecture) 		BEAST 2 Trouble-shooting
(lecture) 		Understanding BEAST 2 XML
(lecture) 		BEAST Clinic
16:45 Welcome Apero Setting Priors
(tutorial) 		BEAST 2 Trouble-shooting
(tutorial) 		XML Hacking
(tutorial) 		Departure
19:00 Dinner Dinner Dinner Dinner Dinner
20:00 Introduction of Participants BEAST Clinic (informal) BEAST Clinic (informal) BEAST Clinic (informal) BEAST Clinic (informal)

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 v2.6 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: