Explains how to use gene_conversion branch on BEAST
We are going to use the development branch of both BEAST and BEAGLE. Assuming you are using mac / linux, the following commands should get you the right versions.
Please follow the BEAGLE installation instructions.
But get the hmc-clock branch.
For mac users, the following commands will compile the CPU version of BEAGLE. Follow the instructions if you need to install any other dependent software.
xcode-select --install
brew install libtool autoconf automake
git clone -b hmc-clock https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
./autogen.sh
./configure --without-opencl --without-cuda
sudo make install
The libraries are installed into /usr/local/lib.
You can find them by ls /usr/local/lib/*beagle*.
The following commands will compile the gene_conversion branch of BEAST.
You may need to install ant by brew install ant through Homebrew.
git clone -b gene_conversion https://github.com/beast-dev/beast-mcmc.git
cd beast-mcmc
ant
This will compile the jar files under beast-mcmc/build/dist/ where you can find beast.jar, beauti.jar and trace.jar.
The example xml file sets up the HKY+IGC model with single IGC parameter for the YEAST ribosomal protein coding genes YLR406C and YDL075W.
Before runnign the xml file, let's look at the command line options for running BEAST.
cd where_you_want_to_run
java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -help
To run the example xml file, try the following lines
cd where_you_want_to_save_output
java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -seed 666 -overwrite where_xml_file_is_stored/first_example.xml
to be continued...