Cipres Science Gateway | BEAST Information

BEAST

BEAST (Bayesian Evolutionary Analysis by Sampling Trees) is a program for Bayesian MCMC analysis of molecular sequences. It is oriented towards inferring rooted, time-measured phylogenies using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. Here BEAST is run using the BEAGLE framework on XSEDE (formerly TeraGrid) machines. In this case, the machine is Trestles at UCSD.

How fast will it Run? See our benchmarks, and explanation here.

BEAST has an extensive user community with a large and sophisticated set of information for use of this program. We refer the user to the BEAST site for the most recent, and best information on use of this program.

Input files: BEAST accepts as input an XML file which configures all parameters for the program. While it is possible to produce such a file manually, this is typically accomplished using the program BEAUti. The CIPRES Science Gateway does not offer tools to create this file yet. This is because the user interface offered by BEAUti is far better than anything we could create with available resources, and because preparation of the input file does not require heroic computational resources, so users can usually install and run this program locally.

Output files:

The table below shows the kinds of results returned by CIPRES Science Gateway:

Input File Names	Sample File from a Test
input file	beast_input.xml

Sample Output File Type	File Name
log file	yourjob.log
tree file(s)	yourjob.trees
operators file	mcmc.operators

In good practice, one conducts multiple runs of the BEAST program, combines the log files, and analyzes them.

There are several auxiliary programs designed to help with the analysis of BEAST results. These include LogCombiner, TreeAnnotator, and TreeLogAnalyzer which can be found on the BEAST site. In addition, the programs Tracer and FigTree were developed independently of BEAST, but are designed to assist in the analysis of BEAST results.

If you use BEAST here, please cite:

Drummond AJ & Rambaut A (2007) "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7, 214 full text
Suchard MA & Rambaut A (2009) "Many-Core Algorithms for Statistical Phylogenetics" Bioinformatics 25, 1370-1376.

If there is a tool or a feature you need, please let us know.