BEAST
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.
License
https://github.com/CompEvol/beast2/blob/master/COPYING
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of beast and load default version of beast as
module avail beast/ # list available modules module load beast # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail beast
and choose explicit version you want to use. Is highly recommended to use BEAST 2.5.0 with SNAPP 1.4.0 because SNAPP 1.3.0 (included in BEAST 2.4.6) contains an issue.
For parallel running are required additional parameters
-instances N -threads N
where N is one less value than number of processors requested in PBS task.
Usage with BEAGLE
# Load BEAST, e.g. module add beast2/beast2-2.6.7-intel-19.0.4-d2lg5zn # Load OpenJDK module add openjdk/openjdk-1.8.0_222-b10-intel-19.0.4-xc66unh # Load BEAGLE module add libbeagle/libbeagle-3.1.2-intel-19.0.4-gpu-m62lgl6 # See available graphical cards (if applicable) and help beast -beagle_info beast -help # Use BEAST with BEAGLE beast ... -beagle ... XXX.xml
See also documentation and work with GPU_clusters (česky).
Documentation
https://www.beast2.org/tutorials/