Scalable Bayesian divergence time estimation with ratio transformations

This repository contains the instructions and files to reproduce the analyses performed in the "Scalable Bayesian divergence time estimation with ratio transformations" paper by Ji et al.

Setting up BEAGLE

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
mkdir build
cd build
cmake -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF ..
sudo make install

For Linux users, the commands are similar.

sudo apt-get install build-essential autoconf automake libtool git pkg-config openjdk-9-jdk
git clone -b hmc-clock https://github.com/beagle-dev/beagle-lib.git
cd beagle-lib
mkdir build
cd build
cmake -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF ..
sudo make install

The libraries are installed into /usr/local/lib. You can find them by ls /usr/local/lib/*beagle*.

Setting up BEAST

The following commands will compile the hmc-clock branch of BEAST.

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

For Mac users, you may need to install ant by brew install ant through Homebrew.

For Linux users, you can install ant by sudo apt-get install ant.

This will compile the jar files under beast-mcmc/build/dist/ where you can find beast.jar, beauti.jar and trace.jar.

Reproducing the analyses

You may use the following commands for each case of the three data sets as described in the manuscript.

Change your working directory to where you want to store the resulting log files first.

cd where_you_want_to_save_results

West Nile Virus

• "time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_Skyline_onlyHeights_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeights_Serial_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_skyline_onlyHeight_Univariable.xml
  

• "rate & time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_HMC_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_Skyline_rateNTime_only_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_Serial_save -overwrite where_this_repository_is_stored/xmls/WNV/WNV_skyline_rateNTime_Univariable.xml
  

Rabies virus

• "time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_onlyHeights_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_onlyHeights_Univariable_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_onlyHeights_Univariable.xml
  

• "rate & time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_HMC_rateNtime_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_rateNTime_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/RRV/RABV_Exp_rateNTime_Univariable_save -overwrite where_this_repository_is_stored/xmls/RRV/RacRABV_Exp_rateNTime_Univariable.xml
  

Lassa Virus

• "time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_onlyHeights_HMC_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_onlyHeights_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_onlyHeights_Univariable_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_onlyHeights_Univariable.xml
  

• "rate & time" scenario

  • HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_rateNTime_HMC_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_rateNTime_HMC.xml
  

  • Univariable

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -load_state where_this_repository_is_stored/xmls/Lassa/Lassa_skygrid_rateNTime_Univariable_save -overwrite where_this_repository_is_stored/xmls/Lassa/Lassa_S_skygrid_rateNTime_Univariable.xml
  

Ebola Virus

• HMC

   java -jar -Djava.library.path=/usr/local/lib where_beast_is_git_cloned/beast-mcmc/build/dist/beast.jar -beagle_CPU -beagle_SSE_off -seed 666 -overwrite where_this_repository_is_stored/xmls/EVD/ebov_HMC_all.xml