{"id":32154426,"url":"https://github.com/juliaphylo/snaq.jl","last_synced_at":"2025-10-21T11:55:40.693Z","repository":{"id":257918579,"uuid":"858876717","full_name":"JuliaPhylo/SNaQ.jl","owner":"JuliaPhylo","description":"Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model","archived":false,"fork":false,"pushed_at":"2025-10-14T15:30:55.000Z","size":4696,"stargazers_count":3,"open_issues_count":13,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-10-21T11:55:32.793Z","etag":null,"topics":["compbio","evolution","networks","phylogenetics"],"latest_commit_sha":null,"homepage":"","language":"Julia","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/JuliaPhylo.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.bib","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2024-09-17T17:27:50.000Z","updated_at":"2025-10-08T21:52:01.000Z","dependencies_parsed_at":"2024-10-26T00:36:03.710Z","dependency_job_id":"e120e86e-15af-4138-928c-ca915b9bd782","html_url":"https://github.com/JuliaPhylo/SNaQ.jl","commit_stats":null,"previous_names":["juliaphylo/snaq.jl"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/JuliaPhylo/SNaQ.jl","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JuliaPhylo%2FSNaQ.jl","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JuliaPhylo%2FSNaQ.jl/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JuliaPhylo%2FSNaQ.jl/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JuliaPhylo%2FSNaQ.jl/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/JuliaPhylo","download_url":"https://codeload.github.com/JuliaPhylo/SNaQ.jl/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/JuliaPhylo%2FSNaQ.jl/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280256225,"owners_count":26299342,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-10-21T02:00:06.614Z","response_time":58,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["compbio","evolution","networks","phylogenetics"],"created_at":"2025-10-21T11:55:36.310Z","updated_at":"2025-10-21T11:55:40.687Z","avatar_url":"https://github.com/JuliaPhylo.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# SNaQ: Maximum pseudolikelihood estimation of species network \u003cimg src=\"docs/src/snaq.png\" align=right title=\"SNaQ logo\" width=262.5 height=111\u003e\n\n|**Documentation**| **Build Status** | **Code Coverage**   | **Style Guide** |\n|:---------------:|:----------------:|:-------------------:|:----------------|\n|[![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]\n\n[docs-stable-img]: https://img.shields.io/badge/docs-stable-blue.svg\n[docs-stable-url]: https://JuliaPhylo.github.io/SNaQ.jl/stable/\n[docs-dev-img]: https://img.shields.io/badge/docs-dev-blue.svg\n[docs-dev-url]: https://JuliaPhylo.github.io/SNaQ.jl/dev/\n\n[build-img]: https://github.com/JuliaPhylo/SNaQ.jl/actions/workflows/CI.yml/badge.svg?branch=main\n[build-url]: https://github.com/JuliaPhylo/SNaQ.jl/actions/workflows/CI.yml?query=branch%3Amain\n[pgkeval-img]: https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/S/SNaQ.svg\n[pgkeval-url]: https://JuliaCI.github.io/NanosoldierReports/pkgeval_badges/S/SNaQ.html\n[aqua-img]: https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg\n[aqua-url]: https://github.com/JuliaTesting/Aqua.jl\n\n[codecov-img]: https://codecov.io/gh/JuliaPhylo/SNaQ.jl/branch/master/graph/badge.svg\n[codecov-url]: https://codecov.io/gh/JuliaPhylo/SNaQ.jl\n\n[style-img]: https://img.shields.io/badge/code%20style-blue-4495d1.svg\n[style-url]: https://github.com/invenia/BlueStyle\n\u003c!-- ColPrac: Contributor's Guide on Collaborative Practices for Community Packages --\u003e\n[colprac-img]: https://img.shields.io/badge/ColPrac-Contributor's%20Guide-blueviolet\n[colprac-url]: https://github.com/SciML/ColPrac\n\n## Overview\n\nSNaQ implements the statistical inference method in Sol\u0026iacute;s-Lemus and An\u0026eacute;\n[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).\nThe procedure involves a numerical optimization of branch lengths and\ninheritance probabilities, and a heuristic search in the space of\nlevel-1 phylogenetic networks.\n\nTo get help, check\n\n- the latest [SNaQ documentation](https://juliaphylo.github.io/SNaQ.jl/dev)\n- the latest [PhyloNetworks documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev)\n- [PhyloUtilities](https://juliaphylo.github.io/PhyloUtilities/) with a step-by-step tutorial from multi-locus sequences to necessary input for SNaQ\n- [tutorial](https://solislemuslab.github.io/snaq-tutorial/) for SNaQ estimation\n  (from a 2023 workshop)\n- the [JuliaPhylo google group](https://groups.google.com/forum/#!forum/juliaphylo-users)\n  for common questions. Join the group to post/email your questions,\n  or to receive information on new versions, bugs fixed, etc.\n- search for answers in\n  [github issues](https://github.com/JuliaPhylo/SNaQ.jl/issues) and\n  post a new issue to post a question or a report potential bugs.\n\n## Overview\n\nSNaQ implements the statistical inference method in Sol\u0026iacute;s-Lemus and An\u0026eacute;\n[(2016)](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896).\nThe procedure involves a numerical optimization of branch lengths and\ninheritance probabilities, and a heuristic search in the space of\nlevel-1 phylogenetic networks.\n\nTo get help, check\n\n- the latest [SNaQ documentation](https://juliaphylo.github.io/SNaQ.jl/dev)\n- the latest [PhyloNetworks documentation](https://juliaphylo.github.io/PhyloNetworks.jl/dev)\n- a [wiki](https://github.com/juliaphylo/PhyloNetworks.jl/wiki) for a\n  step-by-step tutorial with background on networks (last revised 2022)\n- [tutorial](https://cecileane.github.io/networkPCM-workshop/) for\n  comparative methods, including network calibration (2023 workshop)\n- the [google group](https://groups.google.com/g/juliaphylo-users)\n  for common questions. Join the group to post/email your questions,\n  or to receive information on new versions, bugs fixed, etc.\n\n## Citing\n\nFor the SNaQ method in particular, please cite\n- Claudia Sol\u0026iacute;s-Lemus and C\u0026eacute;cile An\u0026eacute; (2016).\n  Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting.\n  [PLoS Genet](http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1005896)\n  12(3):e1005896.\n  [doi:10.1371/journal.pgen.1005896](https://doi.org/10.1371/journal.pgen.1005896)\n\nFor the PhyloNetworks package, please cite:\n- Claudia Solís-Lemus, Paul Bastide and Cécile Ané (2017). \n  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)\n\nSee [`CITATION.bib`](CITATION.bib) for the relevant reference(s).\n\n\u003e [!NOTE]\n\u003e Much of this package was formerly part of PhyloNetworks v0.16.4 (and prior).\n\u003e PhyloNetworks v0.17, v1.0 and later have been stripped of functions\n\u003e implementing the SNaQ method.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuliaphylo%2Fsnaq.jl","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjuliaphylo%2Fsnaq.jl","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjuliaphylo%2Fsnaq.jl/lists"}