Introductory tutorials

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.

Advanced Tutorials

These tutorials tackle a range of advanced, technical, topics. They usually involve editing the BEAST XML configuration files.

Hierarchical Phylogenetic Models

Markov Jumps and Rewards

Epoch Models

Adaptive MCMC

Model Selection

Model Selection — Advanced

Incorporating travel history

Analysing datasets with tens of thousands of taxa