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

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

• Java 8
• sbt

Optionally (but for significant speed-up):

• libpll

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"