BEAST

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Description

BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred 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. We include a simple to use user-interface program for setting up standard analyses and a suit of programs for analysing the results.

Availability

Program is actually available in version BEAST 1.6.1, 1.7.0, 1.7.4, 1.8.2, 2.0.1 and 2.4.6

Use

Program Beast is available in module beast. Load modul ("module add beast" for 2.0.1 and "module add beast-1.6.1" for 1.6.1, or "module add beast-2.4.6") and run "beast" with option (see below) or "babel - help" for help, but firstly run "module add babel" . Usage:

beast [-verbose] [-warnings] [-strict] [-window] [-options] [-working] [-seed] [-prefix <PREFIX>] 
[-overwrite] [-errors <i>] [-threads <i>] [-java] [-beagle] [-beagle_info] [-beagle_order <order>] [-beagle_instances <i>] 
[-beagle_CPU] [-beagle_GPU] [-beagle_SSE] [-beagle_single] [-beagle_double] [-beagle_scaling <default|none|dynamic|always>] 
[-help] [<input-file-name>]

For parallel running are required additional parameters

-beagle_instances N -threads N

where N is one less value than number of processors requested in PBS task.

Documentation

http://beast.bio.ed.ac.uk/ and http://beast2.org

Licence

The complete source code for BEAST is now distributed under the GNU Lesser General Public License and the source code, bug tracking database and information for developers is now hosted by Google:

http://beast-mcmc.googlecode.com/

Supported platforms

Linux 64bit machines ( x86_64 property)

Program administrator

meta@cesnet.cz

Homepage

URL: http://beast2.org