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. Template:App Location
- 1.7.1 (default)
Running the application using modules
To use beast with the environment modules system at HPC the following commands are available:
Get module information for beast:
$module spider beast
Load the default application module:
$module load beast
The modulefile for this software adds the directory with executable files to the shell execution PATH and sets the following environment variables:
- HPC_BEAST_DIR - directory where beast is located.
- HPC_BEAST_BIN - executable directory
- HPC_BEAST_DOC - docs directory
- BEAST - Beast directory
- _JAVA_OPTIONS - Default memory settings (-Xms=512m -Xmx1024m). They can be changed in the job script.
export _JAVA_OPTIONS="-Xms1024m -Xmx2048m"
Beast is also available for use through the friendly web interface of the UF HPC Galaxy instance. It's located in the "Phylogenetics" section.
Interactive beauti use
To connect to a test node, for example biotest, where you can run the graphical beauti software to build an xml file for the BEAST use the following or a similar command on a linux or MacOS X system:
ssh USER@biotest.ufhpc -o ForwardX11=yes -o ForwardX11Trusted=yes -o ProxyCommand='ssh USER@bio.hpc.ufl.edu exec nc biotest %p'
or add the following to your ~/.ssh/config file:
Host biotest User USER KeepAlive yes ProxyCommand ssh USER@bio.hpc.ufl.edu exec nc biotest %p ForwardX11 yes ForwardX11Trusted yes
where USER is your username. After editing ~/.ssh/config you can just run the following command to connect:
Once connected run
module load beast beauti