Download and install BEAST

The first step is to download BEAST and install it. We provide instructions for doing this on the common operating systems. We also recommend installing two additional software packages that are a critical part of BEAST analyses. These are Tracer, for analysing the output of BEAST, and FigTree for viewing the resulting trees and getting them ready for publication.

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
As the name suggests this is probably where you want to start. This tutorial describes the use of BEAUti and BEAST to analyse some primate sequences and estimate a phylogenetic tree. It will take you through the process of importing an alignment, making choices about the model, generating a BEAST XML file. You will then run BEAST.
Second Tutorial
This tutorial follows directly on from the first, looking at the output of BEAST, diagnosing problems and summarising the results. This tutorial will introduce some of the utilities packaged with BEAST, logcombiner and treeannotator, as well as the external applications, Tracer and FigTree.
Estimating Rates and Dates
This tutorial provides a step-by-step tutorial for analyzing a set of virus sequences which have been isolated at different points in time (heterochronous data). The aim of this exercise is to obtain an estimate of the rate of molecular evolution, an estimate of the date of the most recent common ancestor and to infer the phylogenetic relationships with appropriate measures of statistical support.

How-tos

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

Setting tip dates

Analysing BEAST output

Sampling the dates of tips