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• Black box variational inference of evolutionary parameters (node heights and population sizes of each internal node and internal branch) on a species tree under the coalescent with recombination. The data is sequence alignment of recombinant DNA. We estimate node heights in unit of generations and population sizes in unit of individuals. We estimate the mean and standard deviation of the posterior of each parameter.
• We use mspms, an ms-compatible command line interface to the msprime library. Details of installation can be found here. Please make sure mspms (usually in ~/.local/bin) is on your system search path.
• We use BEAGLE, a high-performance library to calculate the "Felsenstein Likelihood". Full details of installation instructions can be found here, always follow "Installing from source".

  • Instructions for installing BEAGLE on Mac OS X

  • Instructions for installing BEAGLE on Windows

  • Instructions for installing BEAGLE on Linux

  • If there is error, try command: java -Djava.library.path="/usr/local/lib" -jar PhyloNet_X.X.X.jar script.nex

    
    

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