Available extensions

Extension Beast package version LPhy extension version Homepage Examples
Phylonco v1.0.0 v0.0.3 https://github.com/bioDS/beast-phylonco phylonco-lphy-examples.zip

Manual installation

Installing the extension

LPhy extensions can be installed manually by downloading the extension jar and placing it inside the lib subdirectory of your LPhy installation location.

For example, to install the Phylonco extension for LPhy:

  1. Go to the releases page of the extension, e.g., Phylonco releases

  2. Download the jar with the prefix -lphy-(version number).jar, for example phylonco-lphy-0.0.3.jar

  3. Place the jar inside the lib subdirectory of your LPhy installation

Your directory structure should look like this:

LPhy libraries
Figure 1: Adding phylonco extension to LPhy libraries.

Loading examples

Examples can be found in the releases page of the extension. To load the examples into LPhy Studio:

  1. Go to the releases page of the extension, e.g., Phylonco releases

  2. Download the file with the suffix *-lphy-examples.zip, e.g., phylonco-lphy-examples.zip

  3. Unzip the *-lphy-examples.zip file inside the examples subdirectory of your LPhy installation. Your directory structure should look like this:

LPhy examples
Figure 2: Adding phylonco to LPhy examples.
  1. Restart LPhy Studio, and these examples will be available through the Menu “File” -> “Example scripts” -> “extensionName”. For the Phylonco extension, this will be available through “File” -> “Example scripts” -> “phylonco”. Loading in the example script gt16CoalErrModel.lphy will display:
Phylonco script
Figure 3: Loading an example Phylonco script.

Installing by extension manager

Extensions can also be installed using the “LPhy Extension Manager” from the Menu in LPhy Studio.

This functionality will be added in future releases.