Shrinkage-based random local clocks with scalable inference

This document outlines the steps necessary to recreate the analyses of Shrinkage-based random local clocks with scalable inference

Setting up BEAST:

1. Ensure you have Java version 1.8 or later installed.
   • From the command line, type java -version.
   • The output should start with java version "1.8.0_<other numbers>".
   • If java is not installed or the wrong version of java is installed, please follow the instructions here.
2. Ensure you have git installed.
   • From the command line, type git --version. The version of git should be returned.
   • If git is not installed, please follow the instructions here.
3. Ensure you have ant installed.
   • From the command line, type ant -version. The version of ant should be returned.
   • If ant is not installed, please follow the instructions here.
4. Download and build BEAST
   • Enter the following on the command line.

git clone https://github.com/beast-dev/beast-mcmc.git
cd beast-mcmc
git checkout hmc-clock
ant

Setting up the BEAGLE library:

• Clone and build the beagle library (see https://github.com/beagle-dev/beagle-lib for reference)

git clone https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
git checkout hmc-clock
./autogen.sh
./configure
make install

Note where the beagle library installs (typically /usr/local/lib)

Running a BEAST XML file:

1. Navigate to the directory with the beast.jar file.
   • From the beast-mcmc directory (see above), enter the following into the command line:

cd build/dist

2. Run an .xml file from the command line * Enter java -jar -Djava.library.path=/usr/local/lib beast.jar path/to/your/file.xml.

   • Note that library.path should point to install location of libhmsbeagle*.so files

   • BEAST should begin running on the command line.

   • The output .log file will be in the ./beast-mcmc/build/dist directory.

3. Use Tracer to view the .log file.
   • Tracer installation and usage instructions can be found here.