BEAST and BEAST2¶

BEAST and BEAST 2 are cross-platform programs for Bayesian phylogenetic analysis of molecular sequences. The beast bundle packages version 1.10.4 of BEAST and version 2.6.3 of BEAST 2.

UFS HPC Usage Example¶

BEAST 2 is the default variant, so the following command can be executed in the terminal to load the bundle:

1	`module load beast`

The BEAST 2 utilities can be run as shown as below:

beast
beauti
densitree
loganalyser
logcombiner
packagemanager
treeannotator

BEAST can be loaded using the following command:

module load beast release=1

The BEAST utilities can be run as shown below:

beast
beauti
loganalyser
logcombiner
treeannotator
treestat

The beast_shell commmand can be used to access a shell in the beast bundle.

1	`beast_shell`

The beast_test command can be run to test the bundle:

1	`beast_test`

The beast_benchmark command can be used to benchmark the bundle:

1	`beast_benchmark`

BEAST 2 Add or Delete packages¶

In the beast_shell terminal the packagemanager command can be used to install a package, for example:

packagemanager -useAppDir -add DENIM

Similarly the floowing can be run to uninstall a package:

packagemanager -useAppDir -del DENIM

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

BEAST¶

BEAST 2¶

Licensing Information¶

BEAST is licensed under the GPLv2.1 license and BEAST 2 is licensed under the GPLv2.1 license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za