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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.
- Java 8 or higher: This is required by BEAST 2 (download).
- 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 v2.5.2 for the workshop (download).
- FigTree: FigTree is a graphical viewer of phylogenetic trees, specifically designed to display summarised 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).
- RStudio (optional): RStudio provides a friendly front-end for R (download).
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.
In addition, the following review papers might be useful:
- Bayesian molecular clock dating of species divergences in the genomics era, Mario dos Reis, Phillip Donoghue, Ziheng Yang
- Evolutionary analysis of the dynamics of viral infectious disease, Oliver Pybus, Andrew Rambaut
- Bayesian molecular dating: opening up the black box, Lindell Bromham, Sebastián Duchêne, Xia Hua, Andrew M. Ritchie, David A. Duchêne, Simon Y. W. Ho