Taming the BEAST Online

Online!
June 07, 2021-June 11, 2021

Workshop Programme

Important: Times are in Central European Summer Time (UTC+2).

Monday Tuesday Wednesday Thursday Friday
09:00 Workshop Welcome Tanja Stadler
Introduction to Phylodynamic Models (slides) 		Remco Bouckaert
Language evolution and phylogeography (slides)		 Denise Kühnert
Modelling epidemics with BEAST 2 (slides)		 Tim Vaughan
Epidemic trajectory inference (slides)
09:15 Alexei Drummond
Introduction to Bayesian Phylogenetics
10:45 Morning Break Morning Break Morning Break Morning Break Morning Break
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 Break Lunch Break Lunch Break Lunch Break Lunch Break
13:30
14:00 Substitution model averaging
(tutorial) 		Bayesian Skyline Plot and Birth-death Skyline Plot
(tutorial) 		LinguaPhy (tutorial) The Structured Coalescent
(lecture, tutorial) 		Inferring recombination graphs with BEAST 2
(lecture, tutorial)
15:45 Afternoon Break Afternoon Break Afternoon Break Afternoon Break Afternoon Break
16:15 Setting Priors
(lecture) 		BEAST 2 Trouble-shooting
(lecture) 		BEAST Clinic Understanding BEAST 2 XML
(lecture) 		BEAST Clinic
16:45 Setting Priors
(tutorial) 		BEAST 2 Trouble-shooting
(tutorial) 		XML Hacking
(tutorial)
18:00 End of Day End of Day

Lecture slides

Slides to lectures are available from here

Required Software

Please ensure the following software is installed prior to the start of the workshop.

  • 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: