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Ancestral Recombination Graph Modelling & Inference in Julia https://patrickfournier.ca/software/documentation/moonshine
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Moonshine.jl Julia

Project Status: Active – The project has reached a usable state and is being actively developed. Documentation stable Documentation dev Aqua QA DOI

Overview

Moonshine.jl is a Julia framework for coalescent modelling oriented towards ancestral recombination graph (ARG) inference. It provides the AbstractGenealogy type which leverages Graphs.jl for convenient implementation of graph-theoretical models of molecular evolution.

Installation

As usual, from julia's REPL, enter Pkg mode by pressing ]. Then,

pkg> add Moonshine

Documentation

This readme is austere by design. Full Documentation as well as a quickstart tutorial are available on a dedicated website. The tutorial is targeted towards experienced as well as first-time julia users.

Roadmap

  • Fix unconstrained recombinations-and-recoalescence simulation
  • Export ARGs as succinct tree sequence
  • Support for missing data
  • Implement SC-style type 2 recombination events

Documentation

  • Complete API documentation
  • Add examples
  • Write guide on how to import data from VCF files

People