Documentation by topics and keywords.
Getting started
Pages to help you get started installing and running BEAST and its associated utilities.
Programs
The programs that make up the BEAST software packages and associated software.
Tutorials
Tutorials to introduce common analyses through a step-by-step walk through.
- Adaptive MCMC Tutorial
- Optimizing Performance
- Using BETS to evaluate temporal signal
- Continuous Phylogeography Tutorial
- Analysing Continuous Traits
- Analysing Continuous Traits without Sequence Data
- Discrete Phylogeography Tutorial
- Discrete Trait Tutorial
- Epoch Model Tutorial
- First Tutorial
- How to setup hierarchical models for sets of parameters
- Markov Jumps and Rewards
- Markov Jumps and Rewards
- Markov-modulated Models Tutorial
- Model Averaging for Clocks Tutorial
- Model Selection Tutorial
- Model Selection Advanced Tutorial
- Online Bayesian Phylodynamic Inference Tutorial
- The evolutionary dynamics of a influenza epidemic
- Revealing the fluctuating evolutionary dynamics of seasonal influenza
- Estimating rates and dates from time-stamped sequences
- Second Tutorial
- Sequential Monte Carlo BEAST Tutorial
- Using TempEst for data exploration
- Approaches for analyzing large phylogenetic datasets
- Time Dependent Rates
- Accommodating individual travel history in discrete phylogeographic diffusion
- Phylogeographic Diffusion in Continuous Space - WNV example
- Phylogeographic Diffusion in Continuous Space - YFV example
- Phylogeographic diffusion in discrete space
- Visualizing phylogenetic trees using FigTree
- Practical genomic epidemiology
- Revealing the evolutionary dynamics of influenza
- Model Selection and Testing
- Estimating rates and dates from time-stamped sequences
- Phylodynamic inference of respiratory viruses
How-tos
These are short tutorials that describe a specific analysis or task.
- Analysing BEAST output using Tracer
- How to specify dates for tips
- Construct a model in BEAUti
- How to create custom substitution models
- How to use empirical sets of trees
- How to create fixed local clock models
- How to create taxon sets
- How to sample the dates of sequences
- Identifying convergence problems using Tracer
Reference Documents