Cipres Science Gateway | BEAST2 Information

BEAST2

BEAST2 (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 machines. In this case, the machine is Gordon at UCSD.

BEAST2 has an extensive user community with a large and sophisticated set of information for use of this program. We refer the user to the BEAST2 site for the most recent, and best information on use of this program. Manuals and Tutorials are available on the BEAST2 site.

Input files: BEAST2 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 BEAST2 program, combines the log files, and analyzes them.

There are several auxiliary programs designed to help with the analysis of BEAST2 results. These include LogCombiner, TreeAnnotator, and TreeLogAnalyzer which can be found on the BEAST2 site. In addition, the programs Tracer and FigTree were developed independently of BEAST2, but are designed to assist in the analysis of BEAST2 results.

If you use BEAST2 here, please cite:

Bouckaert, R., Heled, J., Kühnert, D., Vaughan, T., Wu, C-H., Xie, D., Suchard, MA., Rambaut, A., & Drummond, A. J. (2014). BEAST 2: A Software Platform for Bayesian Evolutionary Analysis. PLoS Computational Biology 10(4)e1003537. doi:10.1371/journal.pcbi.1003537

For BEAGLE, cite:
Suchard MA & Rambaut A (2009) "Many-Core Algorithms for Statistical Phylogenetics" Bioinformatics 25, 1370-1376.

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