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
2017/02/06
Tuesday
2017/02/07
Wednesday
2017/02/08
Thursday
2017/02/09
Friday
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:
Simon Ho
Speaker:
Tracy Heath
Speaker:
David Bryant
Speaker:
Remco Bouckaert
Speaker:
Alexei Drummond
10:30 - 11:00 Morning tea Morning tea Morning tea Morning tea Morning tea
11:00 - 12:30 Tutorial 1a:
Relaxed phylogenetics
Tutorial 2a:
Fossilized birth-death tree prior
Tutorial 3a:
Bayes factor delimitation of species
Tutorial 4a:
Substitution model averaging
Panel discussion and free tutorial session
12:30 - 14:00 Lunch Lunch Lunch Lunch Lunch
14:00 - 14:30 Speaker:
Alexei Drummond
Speaker:
Veronika Bošková
Speaker:
Huw Ogilvie
Speaker:
Tim Vaughan
14:30 - 16:00 Tutorial 1b:
Bayesian Skyline plot
Tutorial 2b:
Troubleshooting and setting priors
Free time for
excursions
Tutorial 4b:
Species trees with StarBEAST2 and calibrated species trees
Tutorial 5b:
Structured coalescent with MultiTypeTree
16:00 - 16:30 Afternoon tea Afternoon tea Afternoon tea Afternoon tea
16:30 - 17:00 Speaker:
Louis du Plessis
Speaker:
Tim Vaughan
Speaker:
David Duchêne
17:00 - 18:30 Tutorial 1c:
Birth-death skyline plot
Tutorial 2c:
Bacter
Tutorial 4c:
Model adequacy
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.

Download

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.

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

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