BEAST is built on a large body of prior work and appropriate citations for individual modules, models and components will be listed when BEAST is run. BEAST-Users mailing list. Users are strongly advised to join the BEAST mailing-list. This will be used to announce new versions and advise users about bugs and problems.

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 common operating systems to provide a user-interface that is ‘native’ and familiar.

BEAST can also import FASTA files (as long as the sequences have been aligned) or BEAST XML files (in which case the data will imported but the models and settings will not). Once loaded, the alignment will be displayed in the main window in a table: If you want to look at the actual alignment, double click on the row in the table.

BEAST can be downloaded from the following link: BEAST X v10.5.0-beta5 - UNIX/Linux version 46.2MB; This will download a compressed tar archive (a ‘.tgz’ file).

BEAST | Bayesian Evolutionary Analysis Sampling Trees. This is the main program that takes a control file generated by BEAUti and performs the analysis.

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

Installing BEAST. Unzip the downloaded compressed ZIP archive (currently BEAST.v10.5.0-beta5.zip). The unzipped files contain executable binaries for BEAST, BEAUti, LogCombiner, TreeAnnotator and TreeStat. Double-clicking on those files will automatically start the corresponding program. BEAGLE acceleration library

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.

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 make use of highly-parallel processors such as those in …

The first step will be to convert an alignment file in fasta format into a BEAST XML input file. This is done using the program BEAUti (this stands for Bayesian Evolutionary Analysis Utility). This is a user-friendly program for setting the evolutionary model and options for the MCMC analysis.