Hamiltonian Monte Carlo on the space of phylogenies
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README.md

phyloHMC

An implementation of Probabilistic Path Hamiltonian Monte Carlo for Bayesian phylogenetic inference.

Prerequisites

phyloHMC is written in Scala. To compile and run, you will need:

Optionally (but for significant speed-up):

To create a standalone jar, compile with the command sbt assembly.

Example

An example dataset is provided.

sbt "run examples/surrogate.phmc examples/primates.fst 1000 1E-2 50"