Taming the BEAST Eh!

Squamish, British Columbia
August 12, 2019-August 16, 2019

Workshop Programme

Sunday
2018/08/11 		Monday
2018/08/12		 Tuesday
2018/08/13 		Wednesday
2018/08/14 		Thursday
2018/08/15 		Friday
2018/08/16
07:00 Arrival Breakfast and Late Registration Breakfast Breakfast Breakfast Breakfast
08:45 Welcome Message
Jeffrey Joy
BC Centre for Excellence in HIV/AIDS 		Housekeeping Housekeeping Housekeeping Housekeeping
09:00 Invited Lecture:
Investigating the Dynamics of Diversification using Molecular Phylogenies
Matthew Pennell
(Univ. of British Columbia)
(slides)		 Invited Lecture:
Bayesian Outbreak Reconstruction with Unsampled Cases and Tree Uncertainty
Caroline Colijn
(Simon Fraser Univ.)
(slides)		 Lecture:
Statistical Models on Phylogenetic Networks
Claudia Solís-Lemus
(slides) 		Lecture:
Divergence Time Estimation and the Fossilized Birth-Death Model
Joëlle Barido-Sottani
(slides) 		Lecture:
Species Evolution accounting for Fossilization and Coalescence
Huw Ogilvie
(slides)
09:45 Lecture:
Tree Priors, Clocks and Skylines
Alexei Drummond
(slides)
10:00 Lecture:
Basic Principles of Statistical Inference
Alexei Drummond
(slides) 		Tutorial 5:
Bayesian Skyline Plot and Birth-Death Skyline Tutorial
Louis du Plessis
(slides, tutorial) 		Tutorial 6:
Fossilized Birth-Death Model
Joëlle Barido-Sottani
(tutorial) 		Tutorial 9:
StarBEAST2 tutorial
Huw Ogilvie
(tutorial)
11:00 Morning Tea & Coffee Morning Tea & Coffee Morning Tea & Coffee Morning Tea & Coffee Morning Tea & Coffee
11:20 Invited Lecture:
Evolutionary History of HBV in the Circumpolar Arctic
Carla Oslowy
(Nat. Microbiology Laboratory / Univ. of Manitoba)
(slides)
11:30 Lecture:
First Steps in BEAST 2
Louis du Plessis
(slides) 		Lecture:
Model Selection and Averaging
Remco Bouckaert
(slides) 		Lecture:
Structured Coalescent Approximations
David Rasmussen
(slides) 		Invited Lecture:
Phylogenetic inferences for Big Data
Claudia Solís-Lemus
(Emory Univ.)
(slides)
12:30 Free Afternoon for Exploring
(Bagged Lunch Provided)
13:00 Lunch Lunch Lunch
Quest University 		Lunch
Quest University
14:00 Tutorial 1:
Relaxed Phylogenetics in BEAST 2
Christiaan Swanepoel
(tutorial) 		Tutorial 3:
Model Averaging
Remco Bouckaert
(tutorial) 		Tutorial 7:
Phylogeography in BEAST 2 (MASCOT)
Remco Bouckaert
(tutorial) 		Troubleshooting Personal Projects and Closing Remarks
15:00 Afternoon Tea & Coffee Afternoon Tea & Coffee Afternoon Tea & Coffee Afternoon Tea & Coffee
15:30 Lecture:
Introduction to Infectious Disease Phylodynamics
David Rasmussen
(slides) 		Lecture:
Troubleshooting and Summarizing BEAST 2 Output
Jūlija Pečerska
(slides)		 Lecture:
Advanced Birth-Death Models
Jūlija Pečerska 		Departure
16:30 Tutorial 2:
Prior Selection and Clock Calibration
Louis du plessis
(slides, tutorial) 		Tutorial 4:
Troubleshooting BEAST 2
Jūlija Pečerska
(tutorial)		 Tutorial 8:
Population Structure using the Multitype Birth-Death Model
Jūlija Pečerska
(tutorial)
17:30
19:00 Welcome & Registration
A-Frame Brewery Co. & Luz Taco Truck 		Dinner Dinner Dinner
Howe Sound Brewery

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 v2.6.0 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: