https://github.com/armanbilge/phylohmc
Hamiltonian Monte Carlo on the space of phylogenies
https://github.com/armanbilge/phylohmc
bayesian-inference hamiltonian-monte-carlo phylogenetics statistics
Last synced: 4 months ago
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Hamiltonian Monte Carlo on the space of phylogenies
- Host: GitHub
- URL: https://github.com/armanbilge/phylohmc
- Owner: armanbilge
- License: agpl-3.0
- Created: 2016-04-07T09:11:56.000Z (about 10 years ago)
- Default Branch: master
- Last Pushed: 2017-04-20T23:25:17.000Z (about 9 years ago)
- Last Synced: 2025-06-09T11:09:48.598Z (about 1 year ago)
- Topics: bayesian-inference, hamiltonian-monte-carlo, phylogenetics, statistics
- Language: Scala
- Homepage: https://arxiv.org/abs/1702.07814
- Size: 128 KB
- Stars: 9
- Watchers: 4
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# phyloHMC
An implementation of [Probabilistic Path Hamiltonian Monte Carlo](https://arxiv.org/abs/1702.07814) for Bayesian phylogenetic inference.
# Prerequisites
phyloHMC is written in Scala. To compile and run, you will need:
* Java 8
* [sbt](http://www.scala-sbt.org/)
Optionally (but for significant speed-up):
* [libpll](https://github.com/xflouris/libpll)
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"
```