LPhyBeast

LPhyBEAST is a command-line program that takes a LPhy script file including model specification and data block, and produces a BEAST 2 XML file. It therefore enables LPhy as an alternative way to succinctly express and communicate BEAST2 analyses.

Setup and usage

LPhyBEAST is implemented as an application in the BEAST 2 package "lphybeast". But you need to add the extra repository https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra.xml to the Package Manager to view it. Follow the instruction to set up, and then use the script lphybeast to create the XML:

A simple usage of LPhyBEAST to create RSV2.xml given the LPhy script RSV2.lphy.

$BEAST_FOLDER/bin/lphybeast tutorials/RSV2.lphy

Create 10 BEAST 2 XMLs for a simple HKY+Coalescent simulation study:

$BEAST_FOLDER/bin/lphybeast -r 10 examples/hkyCoalescent

More scripts are available in linguaPhylo/examples.

Tutorials

LPhy and LPhyBEAST Tutorials

Dependencies

• linguaPhylo

BEAST 2 packages, for example:

• beast2
• BEASTLabs
• feast
• BEAST_CLASSIC
• SMM

The details are in version.xml. All released BEAST 2 packages are listed in Package Viewer.

BEASTLabs beast.util.Script depends on jdk.nashorn.api.scripting.ScriptObjectMirror. If there is NoClassDefFoundError for it, you can add "-Xbootclasspath/a:${nashorn_path}" to your javac, where ${nashorn_path}=/my/path/to/libext/nashorn.jar.

Useful Links

• Developer note