https://github.com/juliaphylo/snaq.jl
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
https://github.com/juliaphylo/snaq.jl
compbio evolution networks phylogenetics
Last synced: 8 months ago
JSON representation
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
- Host: GitHub
- URL: https://github.com/juliaphylo/snaq.jl
- Owner: JuliaPhylo
- License: mit
- Created: 2024-09-17T17:27:50.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-10-14T15:30:55.000Z (8 months ago)
- Last Synced: 2025-10-21T11:55:32.793Z (8 months ago)
- Topics: compbio, evolution, networks, phylogenetics
- Language: Julia
- Homepage:
- Size: 4.48 MB
- Stars: 3
- Watchers: 4
- Forks: 1
- Open Issues: 13
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Citation: CITATION.bib
Awesome Lists containing this project
README
# SNaQ: Maximum pseudolikelihood estimation of species network 
|**Documentation**| **Build Status** | **Code Coverage** | **Style Guide** |
|:---------------:|:----------------:|:-------------------:|:----------------|
|[![stable][docs-stable-img]][docs-stable-url] [![dev][docs-dev-img]][docs-dev-url] | [![build][build-img]][build-url] [![PkgEval][pgkeval-img]][pgkeval-url] [![aqua][aqua-img]][aqua-url] | [![coverage][codecov-img]][codecov-url] | [![Code Style: Blue][style-img]][style-url] [![collaborative][colprac-img]][colprac-url]
[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg
[docs-stable-url]: https://JuliaPhylo.github.io/SNaQ.jl/stable/
[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg
[docs-dev-url]: https://JuliaPhylo.github.io/SNaQ.jl/dev/
[build-img]: https://github.com/JuliaPhylo/SNaQ.jl/actions/workflows/CI.yml/badge.svg?branch=main
[build-url]: https://github.com/JuliaPhylo/SNaQ.jl/actions/workflows/CI.yml?query=branch%3Amain
[pgkeval-img]: https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/S/SNaQ.svg
[pgkeval-url]: https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/S/SNaQ.html
[aqua-img]: https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg
[aqua-url]: https://github.com/JuliaTesting/Aqua.jl
[codecov-img]: https://codecov.io/gh/JuliaPhylo/SNaQ.jl/branch/master/graph/badge.svg
[codecov-url]: https://codecov.io/gh/JuliaPhylo/SNaQ.jl
[style-img]: https://img.shields.io/badge/code%20style-blue-4495d1.svg
[style-url]: https://github.com/invenia/BlueStyle
[colprac-img]: https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet
[colprac-url]: https://github.com/SciML/ColPrac
## Overview
SNaQ implements the statistical inference method in Solís-Lemus and Ané
[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).
The procedure involves a numerical optimization of branch lengths and
inheritance probabilities, and a heuristic search in the space of
level-1 phylogenetic networks.
To get help, check
- the latest [SNaQ documentation](https://juliaphylo.github.io/SNaQ.jl/dev)
- the latest [PhyloNetworks documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev)
- [PhyloUtilities](https://juliaphylo.github.io/PhyloUtilities/) with a step-by-step tutorial from multi-locus sequences to necessary input for SNaQ
- [tutorial](https://solislemuslab.github.io/snaq-tutorial/) for SNaQ estimation
(from a 2023 workshop)
- the [JuliaPhylo google group](https://groups.google.com/forum/#!forum/juliaphylo-users)
for common questions. Join the group to post/email your questions,
or to receive information on new versions, bugs fixed, etc.
- search for answers in
[github issues](https://github.com/JuliaPhylo/SNaQ.jl/issues) and
post a new issue to post a question or a report potential bugs.
## Overview
SNaQ implements the statistical inference method in Solís-Lemus and Ané
[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).
The procedure involves a numerical optimization of branch lengths and
inheritance probabilities, and a heuristic search in the space of
level-1 phylogenetic networks.
To get help, check
- the latest [SNaQ documentation](https://juliaphylo.github.io/SNaQ.jl/dev)
- the latest [PhyloNetworks documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev)
- a [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) for a
step-by-step tutorial with background on networks (last revised 2022)
- [tutorial](https://cecileane.github.io/networkPCM-workshop/) for
comparative methods, including network calibration (2023 workshop)
- the [google group](https://groups.google.com/g/juliaphylo-users)
for common questions. Join the group to post/email your questions,
or to receive information on new versions, bugs fixed, etc.
## Citing
For the SNaQ method in particular, please cite
- Claudia Solís-Lemus and Cécile Ané (2016).
Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.
[PLoS Genet](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896)
12(3):e1005896.
[doi:10.1371/journal.pgen.1005896](https://doi.org/10.1371/journal.pgen.1005896)
For the PhyloNetworks package, please cite:
- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017).
PhyloNetworks: a package for phylogenetic networks. Molecular Biology and Evolution 34(12):3292–3298. [doi:10.1093/molbev/msx235](https://academic.oup.com/mbe/article/34/12/3292/4103410)
See [`CITATION.bib`](CITATION.bib) for the relevant reference(s).
> [!NOTE]
> Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior).
> PhyloNetworks v0.17, v1.0 and later have been stripped of functions
> implementing the SNaQ method.