https://github.com/ps-pat/moonshine.jl

Ancestral Recombination Graph Modelling & Inference in Julia
https://github.com/ps-pat/moonshine.jl

genetics julia

Last synced: 6 months ago
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Ancestral Recombination Graph Modelling & Inference in Julia

• Host: GitHub
• URL: https://github.com/ps-pat/moonshine.jl
• Owner: ps-pat
• License: gpl-3.0
• Created: 2025-04-28T17:37:32.000Z (about 1 year ago)
• Default Branch: master
• Last Pushed: 2025-10-06T18:23:06.000Z (9 months ago)
• Last Synced: 2025-10-06T20:33:27.842Z (9 months ago)
• Topics: genetics, julia
• Language: Julia
• Homepage: https://moonshine.patrickfournier.ca/
• Size: 2 MB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: Readme.md
  • Changelog: CHANGELOG.md
  • License: LICENSE

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README

          
# Moonshine.jl [![Julia](https://img.shields.io/badge/-Julia-9558B2?style=for-the-badge&logo=julia&logoColor=white)](https://julialang.org/)

[![Project Status: Active – The project has reached a usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)

[![Documentation stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://moonshine.patrickfournier.ca/stable/)

[![Documentation dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://moonshine.patrickfournier.ca/dev/)

[![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)

[![DOI](https://zenodo.org/badge/974384938.svg)](https://doi.org/10.5281/zenodo.15558973)

## Overview

Moonshine.jl is a Julia framework for coalescent modelling oriented towards ancestral recombination graph (ARG) inference. It provides the [`AbstractGenealogy`](https://moonshine.patrickfournier.ca/stable/reference/AbstractGenealogy/#Moonshine.AbstractGenealogy) type which leverages [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) for convenient implementation of graph-theoretical models of molecular evolution.

## Installation

As usual, from julia's REPL, enter [Pkg mode](https://docs.julialang.org/en/v1/stdlib/REPL/#Pkg-mode) by pressing `]`. Then,

```julia-repl

pkg> add Moonshine

```

## Documentation

This readme is austere by design. [Full Documentation](https://moonshine.patrickfournier.ca/stable/) as well as a [quickstart tutorial](https://moonshine.patrickfournier.ca/stable/quickstart) 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 sampling

- [ ] Export ARGs as [`succinct tree sequence`](https://tskit.dev/tutorials/what_is.html)

- [ ] 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

* [Patrick Fournier](https://www.patrickfournier.ca) (p_fournier@hushmail.com)

* [Fabrice Larribe](http://fabricelarribe.uqam.ca) (larribe.fabrice@uqam.ca)