HOWTO install BEAST2 packages - The-Bioinformatics-Group/Albiorix GitHub Wiki

BEAST2 can be extended with additional packages such as STACEY or DISSECT. Each user has to install these extensions in their HOME directory using the program beauty that is part of the BEAST2 software suite. The instructions below shows how to install and run an analysis using STACEY:

1. Run the command beauti_2.3.1 (or the version of the program that corresponds to the version of BEAST2 that you want to run).
2. Choose “Manage packages” in the file menu, and install e.g. STACEY (and/or other packages you want to use).
3. Restart beauti_2.3.1 and choose Template->STACEY (or other template)
4. Import alignment, set model, priors etc to make the xml, and then run it with beast_2.3.1.sh

The packages will be installed in ~/.beast.