Hamiltonian Monte Carlo on the space of phylogenies
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An implementation of Probabilistic Path Hamiltonian Monte Carlo for Bayesian phylogenetic inference.
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.
An example dataset is provided.
sbt "run examples/surrogate.phmc examples/primates.fst 1000 1E-2 50"
Hamiltonian Monte Carlo on the space of phylogenies