RootFreqs

BEAST 2 package for specifying equilibrium (root) frequencies that differ from frequencies provided by the site model. A sequence can be specified to define a different distribution at each site. This can be useful for example when a root sequence is known.

The package should work with the following features:

• gamma rate heterogeneity
• proportion invariable sites
• BEAGLE
• ascertainment correction
• ambiguous sites at tips and/or at root
• uncertain sites at tips and/or at root
• threaded likelihood calculation
• with/without an error model at the tips

Installation

Install through BEAUti

Installing the package

Rootfreqs is a BEAST2 package that requires BEAST 2 v2.7. If you have not already done so, you can get BEAST 2 from here.

To install rootfreqs, 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 rootfreqs package is listed, just click on it to select it, and hit the Install/Upgrade button.

If the rootfreqs 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 rootfreqs 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 rootfreqs directory inside BEAST package directory
  • for Windows in Users<YourName>\BEAST\2.X\rootfreqs
  • for Mac in /Users//Library/Application Support/BEAST/2.X/rootfreqs
  • for Linux /home//.beast/2.X/rootfreqs 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 rootfreqs.package.v0.0.2.zip inside the rootfreqs 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/rbouckaert/rootfreqs.git
• Run ant install from the rootfreqs directory

Usage

There is no BEAUti support yet, so you have to edit the XML by hand: see example file for details.