MCPhylo

This package does phylogenetic computations in Julia. It is an extension of the Mamba package which does Markov Chain Monte Carlo (MCMC) sampling for Bayesian analysis. (https://mambajl.readthedocs.io/en/latest/) MCPhylo extends Mamba by a tree module to perform phylogenetic computations.

The goal is to facilitate phylogenetic computations in computational historical linguistics. To facilitate the inference of phylogenetic trees, Probabilistic Path Hamiltonian Dynamics (https://arxiv.org/pdf/1702.07814.pdf) are implemented.

This module is build on a forked instance of Mamba 0.12.0

General Information

The stable version can be installed via the Julia package manager.

using Pkg
Pkg.add("MCPhylo")

In order to use the latest version you can install it directly from its GitHub source.

using Pkg
Pkg.add("https://github.com/erathorn/MCPhylo.jl")

Tree Functionalities

The tree functionalities within this package are reexported from MCPhyloTreehttps://erathorn.github.io/MCPhyloTree.jl/stable/. The the respective documentation for more details.