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BEAST (Bayesian Evolutionary Analysis Sampling Trees) 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.

How to use

To check for versions of beast installed in the system:

$ module avail beast

To run BEAST, first load the module. It is recommended to load modules with specific version. For more details on using modules see our software applications guide.

$ module load beast/1.10.4

Example runs from command-line:

$ java -jar  $BEAST_BASE/lib/beast.jar input.xml
$ java -jar lib/beast.jar -seed 123456 -overwrite input.xml

Where input.xml is the name of a BEAST XML format file. This file can either be created from scratch using a text editor or be created by the BEAUti program from a NEXUS format file.

To know more about creating and tuning the input files look at the documentation and tutorials on-line.

To run with GUI i.e. with -window  option, X environment should be setup. Refer to connecting to Gadi section in documentation.

Beast Arguments



-windowProvide a console window
-optionsDisplay an options dialog
-workingChange working directory to input file's directory
-seedSpecify a random number generator seed
-prefixSpecify a prefix for all output log filenames
-statefileSpecify the filename for storing/restoring the state
-overwriteAllow overwriting of log files
-resumeAllow appending of log files
-errorsSpecify maximum number of numerical errors before stopping
-threadsThe number of computational threads to use (default auto)
-javaUse Java only, no native implementations
-noerrSuppress all output to standard error
-beagleUse beagle library if available
-beagle_infoBEAGLE: show information on available resources
-beagle_orderBEAGLE: set order of resource use
-beagle_instancesBEAGLE: divide site patterns amongst instances
-beagle_CPUBEAGLE: use CPU instance
-beagle_GPUBEAGLE: use GPU instance if available
-beagle_SSEBEAGLE: use SSE extensions if available
-beagle_singleBEAGLE: use single precision if available
-beagle_doubleBEAGLE: use double precision if available
-beagle_scalingBEAGLE: specify scaling scheme to use
-helpPrint this information and stop

Authors: Javed Shaikh, Mohsin Ali
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