Overview
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
Argument | Description |
|---|---|
-window | Provide a console window |
-options | Display an options dialog |
-working | Change working directory to input file's directory |
-seed | Specify a random number generator seed |
-prefix | Specify a prefix for all output log filenames |
-statefile | Specify the filename for storing/restoring the state |
-overwrite | Allow overwriting of log files |
-resume | Allow appending of log files |
-errors | Specify maximum number of numerical errors before stopping |
-threads | The number of computational threads to use (default auto) |
-java | Use Java only, no native implementations |
-noerr | Suppress all output to standard error |
-beagle | Use beagle library if available |
-beagle_info | BEAGLE: show information on available resources |
-beagle_order | BEAGLE: set order of resource use |
-beagle_instances | BEAGLE: divide site patterns amongst instances |
-beagle_CPU | BEAGLE: use CPU instance |
-beagle_GPU | BEAGLE: use GPU instance if available |
-beagle_SSE | BEAGLE: use SSE extensions if available |
-beagle_single | BEAGLE: use single precision if available |
-beagle_double | BEAGLE: use double precision if available |
-beagle_scaling | BEAGLE: specify scaling scheme to use |
-help | Print this information and stop |
Useful Links
http://beast.community/first_tutorial
Authors: Javed Shaikh, Mohsin Ali
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