BEASTShell

BEASTShell is a BEAST 2 package (http://beast2.org)

To use BEASTShell install BEAST first (requires Java 8)

BeanShell scripting for BEAST2. Based on BeanShell 2 (http://code.google.com/p/beanshell2).

To install,

• start BEAUti, which comes with BEAST (http://beast2.org)
• select the "File/Manage pacakges" menu
• select BEASTShell, and click the install button

See http://www.beast2.org/wiki/index.php/Manage_Add-ons for other ways to install BEAST packages and trouble shooting.

To run,

• open the BEAST AppStore,
• double click the BEASTStudio icon

Getting started:

• Introducing BEASTShell: http://blog.beast2.org/2014/05/26/introducing-beastshell/ is a quick-start guide to BEASShell
• Simulation studies with BEASTShell: http://blog.beast2.org/2014/06/02/simulation-studies-with-beastshell shows how to use BEASTShell to run a simulation study in 50 lines of code.
• Roll your own models with BEASTShell: http://blog.beast2.org/2014/06/09/roll-your-own-models-with-beastshell shows hot to define models using BEASTShell for some of the mostly used BEASTObjects.
• Testing with BEASTShell: http://blog.beast2.org/2014/06/16/testing-with-beastshell shows how to test BEAST programs using BEASTShell.

Create BEASTObjects using

bsh % import beast.core.parameter.*;

bsh % x = new RealParameter(value="3.0", dimension=3);

Feedback to [email protected]