{"id":24182986,"url":"https://github.com/ms609/quartet","last_synced_at":"2025-09-21T05:32:04.721Z","repository":{"id":43932665,"uuid":"80424189","full_name":"ms609/Quartet","owner":"ms609","description":"R package to calculate the similarity of two trees based on the number of shared four-taxon subtrees (or splits)","archived":false,"fork":false,"pushed_at":"2025-09-01T08:39:48.000Z","size":15469,"stargazers_count":16,"open_issues_count":10,"forks_count":5,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-09-05T10:08:14.374Z","etag":null,"topics":["bioinformatics","comparison","cran","phylogenetic-trees","phylogenetics","quartet","quartet-distance","research-tool","tree"],"latest_commit_sha":null,"homepage":"https://ms609.github.io/Quartet/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ms609.png","metadata":{"files":{"readme":"README.md","changelog":"NEWS.md","contributing":"CONTRIBUTING.md","funding":null,"license":null,"code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":"codemeta.json","zenodo":null}},"created_at":"2017-01-30T13:34:42.000Z","updated_at":"2025-09-01T08:39:52.000Z","dependencies_parsed_at":"2022-09-08T05:52:12.612Z","dependency_job_id":"0a25870e-cce6-4fd7-92bc-35b14369fb9f","html_url":"https://github.com/ms609/Quartet","commit_stats":{"total_commits":758,"total_committers":6,"mean_commits":"126.33333333333333","dds":0.09630606860158308,"last_synced_commit":"7ce55d5c0867c6c67a3f8eabb93627a2917fb8c8"},"previous_names":[],"tags_count":12,"template":false,"template_full_name":null,"purl":"pkg:github/ms609/Quartet","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FQuartet","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FQuartet/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FQuartet/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FQuartet/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/Quartet/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FQuartet/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":276195628,"owners_count":25601152,"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":"2025-09-21T02:00:07.055Z","response_time":72,"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":["bioinformatics","comparison","cran","phylogenetic-trees","phylogenetics","quartet","quartet-distance","research-tool","tree"],"created_at":"2025-01-13T08:45:55.615Z","updated_at":"2025-09-21T05:32:04.362Z","avatar_url":"https://github.com/ms609.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Project Status: Inactive.](https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)\n[![Build Status](https://github.com/ms609/Quartet/actions/workflows/R-CMD-check.yml/badge.svg)](https://github.com/ms609/Quartet/actions)\n[![codecov](https://codecov.io/gh/ms609/Quartet/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ms609/Quartet)\n[![CRAN Status Badge](https://www.r-pkg.org/badges/version/Quartet)](https://cran.r-project.org/package=Quartet)\n[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/Quartet)](https://cran.r-project.org/package=Quartet)\n[![DOI](https://zenodo.org/badge/80424189.svg)](https://zenodo.org/badge/latestdoi/80424189)\n\n# Quartet\n\n'[Quartet](https://ms609.github.io/Quartet/)' is an R package that calculates \nthe quartet distance between two trees (Estabrook _et al._ 1985),\na measure of their similarity based on the number of shared four-taxon subtrees.\n\nThe quartet distance outperforms a number of widely used tree distances \n(e.g. the Robinson–Foulds, path, and rearrangement distances) against a number\ntheoretical and practical measures (Steel \u0026 Penny 1993; Smith 2020),\nand is particularly valuable in the construction of tree spaces (Smith 2021).\n\n'Quartet' uses the 'tqDist' algorithm (Brodal _et al._ 2004; Sand _et al._ 2014).\nUnlike many other implementations, it distinguishes between quartets that are\ncontradicted by one tree,\nand quartets that are simply absent due to a lack of resolution (i.e.\nthe presence of polytomies; see Smith 2019).\n'Quartet' makes this distinction in both the quartet metric (function\n`QuartetStatus()`) and the partition metric (i.e. Robinson-Foulds distance;\nfunction `SplitStatus()`).\n\n## Using the package\nInstall and load the library from CRAN as follows:\n```\ninstall.packages('Quartet')\nlibrary('Quartet')\n```\n\nFor the latest features, install the development version:\n```r\nif(!require(\"curl\")) install.packages(\"curl\")\nif(!require(\"remotes\")) install.packages(\"remotes\")\nremotes::install_github(\"ms609/Quartet\")\n```\n\nYou will need [Rtools](https://cran.r-project.org/bin/windows/Rtools/) installed \nin order to build the development version from source.\n\nView the [function reference](https://ms609.github.io/Quartet/reference/)\nand [basic usage instructions](https://ms609.github.io/Quartet/articles/Using-Quartet.html).\n\n## Known limitations\n\nQuartet supports trees with up to 477 leaves.  Larger trees contain more \nquartets than can be represented by R's signed 32-bit integers.\nThe underlying 'tqDist' library may handle trees with up to 568 leaves,\nand 64-bit integer representations could increase this number further.  \nMaking either of these improvements within the R package \nwould require substantial additional work, but could be implemented -- do\n[file an issue](https://github.com/ms609/Quartet/issues/new/) if this would be\nuseful to you.\n\n## References\n\n- Brodal G.S., Fagerberg R., Pedersen C.N.S. 2004. Computing the quartet \n  distance between evolutionary trees in time O(_n_ log _n_). \n  Algorithmica 38:377–395.\n\n- Estabrook G.F., McMorris F.R., Meacham C.A. 1985. Comparison of undirected \n  phylogenetic trees based on subtrees of four evolutionary units. \n  Syst. Zool. 34:193–200.\n\n- Sand A., Holt M.K., Johansen J., Brodal G.S., Mailund T., Pedersen C.N.S. 2014.\n  tqDist: a library for computing the quartet and triplet distances between \n  binary or general trees. \n  Bioinformatics 30:2079–2080. https://doi.org/10.1093/bioinformatics/btu157\n\n- Smith, M.R. 2019. Bayesian and parsimony approaches reconstruct \n  informative trees from simulated morphological datasets. Biol. Lett.\n  15:20180632. https://doi.org/10.1098/rsbl.2018.0632\n\n- Smith, M.R. 2020. Information theoretic generalized Robinson–Foulds metrics \n  for comparing phylogenetic trees. Bioinformatics, 36:5007–5013.\n  https://dx.doi.org/10.1093/bioinformatics/btaa614\n\n- Smith, M.R. 2022. Robust analysis of phylogenetic tree space. \n  Systematic Biology, syab100.\n  https://dx.doi.org/10.1093/sysbio/syab100\n\n- Steel, M. and Penny, D. 1993. Distributions of tree comparison metrics:\n  some new results. Syst. Biol. 42: 126-141.\n  https://doi.org/10.1093/sysbio/42.2.126\n\nPlease note that the 'Quartet' project is released with a\n[Contributor Code of Conduct](https://ms609.github.io/Quartet/CODE_OF_CONDUCT.html).\nBy contributing to this project, you agree to abide by its terms.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Fquartet","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Fquartet","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Fquartet/lists"}