BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed …

FigTree is a program for viewing trees, including summary information produced by TreeAnnotator, and producing publication quality figures.

Running BEAST for the first time This tutorial will guide you through running BEAST and some of its accessory programs to do a simple phylogenetic analysis. If you haven’t already, download and …

Tracer (now at version 1.7.2) is a software package for visualising and analysing the MCMC trace files generated through Bayesian phylogenetic inference. Tracer provides kernel density estimation, …

Installing BEAST BEAST has been developed in Java, which allows the same code to run on any platform that has the Java software installed. We have also created packages for each of the …

Using BEAGLE with BEAST BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics package. It can …

Downloading and installing BEAST on Windows BEAST is a software package for phylogenetic analysis with an emphasis on time-scaled trees.

To inform BEAUti/BEAST about the sampling dates of the sequences, go to the Tips menu and select the “Use tip dates” option. By default all the taxa are assumed to have a date of zero (i.e. the …

Click Copy and open the link in a new browser tab/window. To summarise Bayes factor support for rates, select the Discrete Rates tab. Load the output BEAST file containing the spatial rates and rate …

BEASTGen can also be used to create BEAST XML files (as its name suggests). A template can be based on a BEAST XML file and be used to ‘insert’ data from another data file to create a file ready …