Taming the BEAST in London

Rose Room, London School of Hygiene & Tropical Medicine, Keppel Street, London, United Kingdom
July 24, 2017-July 28, 2017

Programme

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

   |  Monday <br> 2017/07/24   | Tuesday <br> 2017/07/25 | Wednesday <br> 2017/07/26 | Thursday <br> 2017/07/27 | Friday <br> 2017/07/28  -------| -------- | -------- | --------|-----------|----------|-------- 08:15  | Welcome and organisation | _Announcements_ | _Announcements_ | _Announcements_ | _Announcements_  08:30  | _Introduction of instructors and participants_ |  **Alexei Drummond:** <br> _Tree priors, clocks and skylines_ |  **Tim Vaughan:** <br> _Modelling structured populations_ <br> **Huw Ogilvie** <br>_Multi-species coalescent inference_ |  **Tanja Stadler:** <br> _Modelling birth-death processes_ | **Erik Volz:** <br> _Pathogen source attribution_ <br>  **Nuno Faria:** <br> _Real-time phylodynamics_ 10:30  | _Coffee break_ | _Coffee break_ | _Coffee break_ | _Coffee break_ | _Coffee break_  11:00  | **Oliver Pybus:** <br> _Basic principles of statistical inference_ <br> **Louis du Plessis:** <br> _Bayesian phylogenetics in BEAST 2_  |  **Louis du Plessis:** <br> _Model averaging, selection and adequacy_ <br>  **Tutorial 2a:** <br> [Substitution model averaging](/tutorials/Substitution-model-averaging)  |  **Nicola Müller:** <br> _Structured coalescent  approximations_ <br> **Tutorial 3a:** <br> [Phylogeography in BEAST2 with MASCOT](/tutorials/Mascot-Tutorial/)  |  **BEAST Clinic:** <br> _Personal projects <br> and troubleshooting_      | **Nicola de Maio:** <br> _Transmission tree reconstruction_ <br> **Tutorial 5a:** <br> [Transmission tree inference in BEAST2 with SCOTTI](/tutorials/SCOTTI-Tutorial/) 13:00  | _Lunch_       | _Lunch_       | _Lunch_      | _Lunch_        | _Lunch_       14:00  | **Oliver Pybus:** <br> _Introduction to infectious disease phylodynamics_ <br> **Tutorial 1a:** <br> [Relaxed phylogenetics in BEAST 2](/tutorials/Introduction-to-BEAST2/) <br> | **Stéphane Hué:** <br> _Troubleshooting the BEAST_ <br> **Tutorial 2b and 2c:** <br> [Skyline plots](/tutorials/Skyline-plots/) and <br> [Troubleshooting](/tutorials/Troubleshooting)  |  **Tutorial 3b and 3c:** <br> [Species trees with StarBEAST2](/tutorials/species-tree-clocks/) and [calibrated species trees](/tutorials/calibrated-species-trees/)    | **Joëlle Barido-Sottani:** <br> _The fossilized birth-death<br>process_ <br> **Tutorial 4b:** <br> [Dating species divergences with the fossilized birth-death process](/tutorials/FBD-tutorial/) | **Tim Vaughan:** <br> _Inferring bacterial recombination graphs_ <br> **Tutorial 5b:** <br> [Bacterial phylogenetics in BEAST 2 with BACTER](/tutorials/Bacter-Tutorial)   16:00  | _Afternoon tea_ | _Afternoon tea_ |  _Free time for excursions_      | _Afternoon tea_         | _Afternoon tea_  16:30  | **Stéphane Hué:** <br> _Setting priors and initial values_ <br> **Tutorial 1b:** <br> [Prior selection and clock calibration](/tutorials/Prior-selection/)   | **BEAST Clinic:** <br> _Personal projects and troubleshooting_      |      | **Jūlija Pečerska:** <br> _Advanced birth-death models_ <br><br> **Tutorial 4a:** <br> [Population structure using the multitype birth-death model](/tutorials/Structured-birth-death-model/)  |  <br> _General discussion and closure_ <br><br> _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…)