Squamish BEAST Tamers

Squamish, British Columbia
August 14, 2023-August 18, 2023

Workshop Programme

Invited talks Lectures Tutorials Interactive
Sunday
2023/08/13 		Monday
2023/08/14		 Tuesday
2023/08/15 		Wednesday
2023/08/16 		Thursday
2023/08/17 		Friday
2023/08/18
08:45 Arrival Welcome Message
Jeffrey Joy
(BCCfE in HIV/AIDS)		 Housekeeping Housekeeping Housekeeping Housekeeping
09:00 Alexei Drummond
Tree priors, clocks and skylines
 Ailene MacPherson
(Simon Fraser University) 		Jūlija Pečerska
(Zürich University of Applied Sciences) 		Sungsik (Kevin) Kong
(UW Madison)
09:15 Alexei Drummond
Introduction to Bayesian phylogenetics
09:30 David Rasmussen
(NC State University)
09:45
10:00 Break Break Break Break Break
10:15 Louis du Plessis
First steps in BEAST2
 Michael Martin
(Johns Hopkins University)		 Joëlle Barido-Sottani
Divergence time estimation
 Huw Ogilvie
Species tree inference and the multispecies coalescent
 Remco Bouckaert
Model selection and model averaging
10:30
10:45
11:00 Coffee Break Coffee Break Coffee Break Coffee Break Coffee Break
11:15
11:30 Introduction to BEAST2
(tutorial)		 Inference of past population dynamics using skyline models
(BEAST2 tutorial ,LPhyBEAST tutorial)		 Dating species divergences with the fossilized birth-death process
(tutorial)		 Estimating species trees using StarBEAST2
(tutorial)		 Substitution model averaging
(tutorial)
11:45
12:00
12:15
12:30 Lunch
Howe Sound Brewery 		Lunch
Howe Sound Brewery 		Collect packed lunch Lunch
Howe Sound Brewery 		Lunch
Howe Sound Brewery
12:45
13:00 Free afternoon
13:15
13:30 Caroline Colijn
(Simon Fraser University)		 Jūlija Pečerska
Troubleshooting in BEAST2
 Joëlle Barido-Sottani &
David Rasmussen
Structured models in phylodynamics

 Free Q&A session
(optional)
13:45
14:00 BEAST2 convergence
(tutorial)
14:15
14:30 Coffee Break BEAST2 initialization
(tutorial)		 Coffee Break Departure
14:45
15:00 Prior selection and clock calibration
(tutorial)		 Coffee Break Parameter and state inference using the approximate structured coalescent
(BEAST2 tutorial, ,LPhyBEAST tutorial)
15:15
15:30 Alexei Drummond
LinguaPhylo
15:45
16:00 Participant introductions and flash talks
 Population structure using the multi-type birth-death model
(tutorial)
16:15
16:30 Ancestral state reconstruction using discrete phylogeography
(LPhyBEAST tutorial)
16:45
17:00 BEAST clinic
(optional)
17:15
17:30 BEAST Clinic
(optional)
17:45
18:00 Welcome event
A-Frame Brewing & Flipside Burgers 		Dinner
Howe Sound Brewery 		Dinner
Howe Sound Brewery 		Dinner
Beach BBQ 		Farewell dinner
Free Bird

Instructors

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 v2.7 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: