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* |
Slides to lectures are available from here
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.
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.
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…)