CCD Package for BEAST 2

Implementation of the conditional clade distribution (CCD) with two parametrisations, namely, based on clade split frequencies (CCD1) and clade frequencies (CCD0). Furthermore, point estimators based on the CCDs are implemented, which allows TreeAnnotator to produce better summary trees than via MCC trees (which is restricted to the sample).

Install through BEAUti

Installing the package

CCD is a BEAST2 package that requires BEAST 2 v2.7.6. If you have not already done so, you can get BEAST 2 from here.

To install CCD, it is easiest to start BEAUti (a program that is part of BEAST), and select the menu File/Manage packages. A package manager dialog pops up, that looks something like this:

If the CCD package is listed, just click on it to select it, and hit the Install/Upgrade button.

If the CCD package is not listed, you may need to add a package repository by clicking the Package repositories button. A window pops up where you can click Add URL and add https://raw.githubusercontent.com/CompEvol/CBAN/master/packages-extra-2.7.xml in the entry. After clicking OK, the dialog should look something like this:

Click OK and now CCD should be listed in the package manager (as in the first dialog above). Select and click Install/Upgrade to install.

Install by hand

• Download the package from here
• Create CCD directory inside BEAST package directory
  • for Windows in Users<YourName>\BEAST\2.X\VSS
  • for Mac in /Users//Library/Application Support/BEAST/2.X/VSS
  • for Linux /home//.beast/2.X/VSS Here is the username you use, and in “2.X” the X refers to the major version of BEAST, so 2.X=2.7 for version 2.7.6.
• Unzip the file CCD.package.v0.0.1.zip inside the CCD directory

Build from code

• Get code for beast2, BeastFX and CCD repositories:
  • git clone https://github.com/CompEvol/beast2.git
  • git clone https://github.com/CompEvol/BeastFX.git
  • git clone https://github.com/CompEvol/CCD.git
• Run ant install from the CCD directory

Usage

Start TreeAnnotator, and select MAP (CCD0) from the drop down box next to Target tree type:

From a terminal, to use CCD0 for Linux and OS X run

/path/to/beast/bin/treeannotator -topology CCD0 input.trees output.tree

where /path/to the path to where BEAST is installed. For Windows, use

\path\to\BEAST\bat\treeannotator.bat -topology CCD0 input.trees output.tree

For CCD1 based point estimates select MAP (CCD1) from the drop down box in the GUI, or use CCD1 instead of CCD0 for the command line version.