BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. It includes a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.
You will need to attend the workshop with BEAST2 installed on your own laptop. Download BEAST2 here.
The workshop will provide a brief introduction to the basics and then move on to more advanced/novel features. Thus, it will be assumed that participants have a basic knowledge of BEAST. For those that do not, and to get the most out of the workshops, we recommend taking a look over the user guides and basic tutorials:
BEAST and
BEAST2. People unfamiliar with the terms
Bayesian,
Phylogenetic or
Inference may want to to do some reading before attending eg.
Phylogenetics,
Bayesian inference,
Phylogenetic tree
Workshop outline (45-60 minutes per session with approx. 20-30 min break between each session):
Part 1 - Introduction (~45 minutes)
This part will include a brief introduction to the the models we use in Bayesian phylogenetic inference. Joseph will talk about the Kingman coalescent, Pure birth and birth death models and substitution and clock models. After that disscussion will move to Inference of population size and the multi-species coalescent and inference of species trees. The later part of this "Introduction" will be quite technical.
Part 2 - Advanced Topics (~45 minutes)
This part includes discussion of Species trees in the presence of migration, Model calibration and calibrated tree priors, exploring the BEAST prior, post analysis, and visualising species and gene trees.
Part 3 - BEAST tutorial (~1 hour)
Participants will generate and run a BEAST analysis and visualize the results on their personal laptop. The tutorial will use
BEAST2. This will also cover the lower level details, time permitting.
The workshop is FREE, but you need to register with
Mitzy Pepper by 3 April 2013
