To help you get started with BEAST and get familiar with the different components and the work-flow we have put together a series of introductory tutorials that you can work through.
- First Tutorial
- An introductory tutorial about running BEAST.
- Second Tutorial
- An introductory tutorial about interpreting BEAST output.
- Estimating Rates and Dates
- A basic tutorial on inferring rates and dates from tip-dated virus data.
- Using TempEst for data exploration
- This tutorial describes the use of TempEst to examine the temporal signal of a data set and to look for problematic or erroneous sequences.
Tutorials for particular types of analyses
- The evolutionary dynamics of a influenza epidemic
- An introduction to phylodynamic analysis using the 2009 H1N1 influenza pandemic.
- Revealing the fluctuating evolutionary dynamics of seasonal influenza
- The phylodynamics of seasonal H3N2 over several seasons using the Skygrid demographic model.
We also provide a number of stand-alone ‘how-to’ documents which describe the procedures for specific analyses, data types, or models in greater detail.
- Creating taxon sets
- How to create a taxon set in BEAUti.
- Setting tip dates
- How to use BEAUti’s options to conveniently set the dates of sequences.
- Analysing BEAST output
- How to analyse the output of BEAST in Tracer
- Sampling the dates of tips
- How to sample uncertainty in the dates of sequences.
- Fixed local clocks
- How to set up the local clock model where different clades have different rates of evolution.
- Custom substitution models
- How to set up a range of nucleotide substitution models that are not amongst the pre-set choices.
These tutorials tackle a range of advanced, technical, topics. They usually involve editing the BEAST XML configuration files.