Programme
Participants are expected to arrive between 18:00 and 19:00 on Sunday, 2017/02/05, followed by a garden BBQ at Venue Waiheke.
| Monday <br> 2017/02/06 | Tuesday <br> 2017/02/07 | Wednesday <br> 2017/02/08 | Thursday <br> 2017/02/09 | Friday <br> 2017/02/10 --------------| -------- | -------- | --------|-----------|----------|--------
| Bayesian phylogenetics and relaxed clocks | Phylodynamics: macroevolution + infectious disease | Species tree and gene trees | Phylogenetic model comparison, selection averaging | Phylogeography and trait evolution 08:30 - 10:30 | Speaker: <br> **Simon Ho** | Speaker: <br> **Tracy Heath** | Speaker: <br> **David Bryant** | Speaker: <br> **Remco Bouckaert** | Speaker: <br> **Alexei Drummond** 10:30 - 11:00 | _Morning tea_ | _Morning tea_ | _Morning tea_ | _Morning tea_ | _Morning tea_ 11:00 - 12:30 | Tutorial 1a: <br> [Relaxed phylogenetics](/tutorials/Introduction-to-BEAST2/) | Tutorial 2a: <br> [Fossilized birth-death tree prior](/tutorials/FBD-tutorial/) | Tutorial 3a: <br> [Bayes factor delimitation of species](https://github.com/BEAST2-Dev/beast-docs/releases/download/v1.0/BFD-tutorial-2017.zip) | Tutorial 4a: <br> [Substitution model averaging](/tutorials/Substitution-model-selection) | Panel discussion and free tutorial session 12:30 - 14:00 | _Lunch_ | _Lunch_ | _Lunch_ | _Lunch_ | _Lunch_ 14:00 - 14:30 | Speaker: <br> **Alexei Drummond** | Speaker: <br> **Veronika Bošková** | | Speaker: <br> **Huw Ogilvie** | Speaker: <br> **Tim Vaughan** 14:30 - 16:00 | Tutorial 1b: <br> [Bayesian Skyline plot](/tutorials/Skyline-plots/) | Tutorial 2b: <br> [Troubleshooting](/tutorials/Troubleshooting) and [setting priors](/tutorials/Prior-selection) | *Free time for<br>excursions* | Tutorial 4b: <br> [Species trees with StarBEAST2](/tutorials/species-tree-clocks/) and [calibrated species trees](/tutorials/calibrated-species-trees/) | Tutorial 5b: <br> [Structured coalescent with MultiTypeTree](/tutorials/Structured-coalescent/) 16:00 - 16:30 | _Afternoon tea_ | _Afternoon tea_ | | _Afternoon tea_ | _Afternoon tea_ 16:30 - 17:00 | Speaker: <br> **Louis du Plessis** | Speaker: <br> **Tim Vaughan** | | Speaker: <br> **David Duchêne** | 17:00 - 18:30 | Tutorial 1c: <br> [Birth-death skyline plot](/tutorials/Skyline-plots/) | Tutorial 2c: <br> [Bacter](/tutorials/Bacter-Tutorial) | | Tutorial 4c: <br> [Model adequacy](/tutorials/adequacy_tutorial/) | _Departure_ 19:00 | *Gourmet fish & chips at Venue Waiheke* | *Dinner at Charlie Farleys* | | *Dinner at the Goldie Room* |
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
BEAST2 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 v2.4.5 for the workshop.
FigTree
FigTree is a graphical viewer of phylogenetic trees, specificly designed to display summarized and annotated trees produced by BEAST. Allows visual analysis of trees.
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.
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.
Java 8 JDK
This Java SE Developlment Kit is required for BEAST 2.
RStudio (optional)
RStudio IDE is a user interface for R.