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:
- Java 8
- sbt
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"