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  1. bdTreeSim bdTreeSim Public

    Simulate phylogenetic trees from a birth-death model conditioned on sampling times

    R

  2. periodic-bottlenecks periodic-bottlenecks Public

    Supporting code for the paper 'Bottlenecks can constrain and channel evolutionary paths'

    Jupyter Notebook

  3. PPMmodelPangenome PPMmodelPangenome Public

    Inference and simulation tools for the Persistant-Private-Mobile model for bacterial pangenome evolution

    C++