{"id":24182995,"url":"https://github.com/ms609/treesearch","last_synced_at":"2025-09-21T05:32:06.950Z","repository":{"id":39498749,"uuid":"98171642","full_name":"ms609/TreeSearch","owner":"ms609","description":"R package for phylogenetic tree search under inapplicable-corrected parsimony and custom optimality criteria","archived":false,"fork":false,"pushed_at":"2025-09-19T13:16:16.000Z","size":128951,"stargazers_count":8,"open_issues_count":51,"forks_count":4,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-09-19T15:36:41.152Z","etag":null,"topics":["bioinformatics","morphological-analysis","phylogenetics","r-package","research-tool","tree-search"],"latest_commit_sha":null,"homepage":"https://ms609.github.io/TreeSearch/","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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":"LICENSE","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2017-07-24T09:09:45.000Z","updated_at":"2025-09-19T13:50:05.000Z","dependencies_parsed_at":"2024-02-29T14:48:41.266Z","dependency_job_id":"d720de76-e2e3-4db4-a831-08848a1edc44","html_url":"https://github.com/ms609/TreeSearch","commit_stats":{"total_commits":1796,"total_committers":6,"mean_commits":299.3333333333333,"dds":"0.24888641425389757","last_synced_commit":"e6b1b8d25dcb0e3356c0966ba6eb7fe5cfc915db"},"previous_names":[],"tags_count":32,"template":false,"template_full_name":null,"purl":"pkg:github/ms609/TreeSearch","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeSearch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeSearch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeSearch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeSearch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/TreeSearch/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeSearch/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":276195629,"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","morphological-analysis","phylogenetics","r-package","research-tool","tree-search"],"created_at":"2025-01-13T08:45:56.952Z","updated_at":"2025-09-21T05:32:06.941Z","avatar_url":"https://github.com/ms609.png","language":"R","readme":"# TreeSearch\n\n  [![codecov](https://codecov.io/gh/ms609/TreeSearch/branch/master/graph/badge.svg)](https://codecov.io/gh/ms609/TreeSearch)\n[![CRAN Status Badge](http://www.r-pkg.org/badges/version/TreeSearch)](https://cran.r-project.org/package=TreeSearch)\n[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/TreeSearch)](https://ms609.github.io/usage/#treesearch)\n[![CRAN RStudio mirror downloads](http://cranlogs.r-pkg.org/badges/grand-total/TreeSearch)](https://ms609.github.io/usage/#treesearch)\n[![DOI](https://zenodo.org/badge/98171642.svg)](https://zenodo.org/badge/latestdoi/98171642)\u003c!--[![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.](http://www.repostatus.org/badges/latest/inactive.svg)](http://www.repostatus.org/#inactive)\n--\u003e\n[![Project Status: Active – – The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)\n\n\"TreeSearch\" (Smith 2023) is an R package that contains a \"shiny\" user interface for \ninteractive tree search and exploration of results, including character\nvisualization,\n[rogue taxon detection](https://ms609.github.io/Rogue) (Smith 2022a),\n[tree space mapping](https://ms609.github.io/TreeDist/articles/treespace.html)\n(Smith 2022b),\nand cluster consensus trees.\n\nInapplicable character states are handled using the algorithm of Brazeau,\nGuillerme and Smith (2019) using the \"Morphy\" C library (Brazeau _et al_. 2017).\nImplied weighting (Goloboff, 1993),\nProfile Parsimony (Faith and Trueman, 2001)\nand Successive Approximations (Farris, 1969)\nare implemented; \n[custom optimality criteria](https://ms609.github.io/TreeSearch/articles/custom.html)\nand search approaches can also be defined.\n\n\n# Installing in R\n\nFull installation instructions, including notes on installing R, are available\nin a [vignette](https://ms609.github.io/TreeSearch/articles/getting-started.html).\n\nInstall and load the stable version from CRAN as follows:\n\n```r\ninstall.packages(\"TreeSearch\")\nlibrary(\"TreeSearch\")\n# Launch the Shiny App with:\nTreeSearch::EasyTrees()\n```\n\nInstall and load the development version of \"TreeSearch\" with:\n\n```r\nif(!require(\"curl\")) install.packages(\"curl\")\nif(!require(\"remotes\")) install.packages(\"remotes\")\nremotes::install_github(\"ms609/TreeSearch\")\nlibrary(\"TreeSearch\")\n```\n\n# Installing stand-alone application\n\nThe TreeSearch user interface can be run as a stand-alone application without\ninstalling R.\n[Download](https://github.com/ms609/TreeSearch/releases) the latest release for your platform.\nIf your preferred platform is not supported, please contact the maintainer.\n\n## Installation on Windows\n\nYou may need to obtain the [ffmpeg library](https://community.chocolatey.org/packages/ffmpeg)\nbefore you can run TreeSearch.\n\nThis is best installed using ['Chocolatey'](https://chocolatey.org/).\n\nOnce chocolatey is installed, open a PowerShell window with administrative privileges, and\ntype `choco install ffmpeg`; then restart your computer.\n\n\n# Quick start\n\nLaunch a graphical user interface by typing `TreeSearch::EasyTrees()` in the R console.\n\nFor more control over search settings, see [`?MaximizeParsimony()`](https://ms609.github.io/TreeSearch/reference/MaximizeParsimony.html).\n\n![Flow charts listing common actions facilitated by TreeSearch](man/figures/Flow.svg)\n\n# Documentation\n\n- [Package functions](https://ms609.github.io/TreeSearch/reference) reference manual\n- [Getting started](https://ms609.github.io/TreeSearch/articles/getting-started.html)\n- [Using the GUI](https://ms609.github.io/TreeSearch/articles/tree-search.html)\n- [Analysing tree spaces](https://ms609.github.io/TreeSearch/articles/tree-space.html)\n- [Loading phylogenetic data into R](https://ms609.github.io/TreeTools/articles/load-data.html)\n- [Parsimony search with inapplicable data](https://ms609.github.io/TreeSearch/articles/tree-search.html)\n\n- [Calculating concavity profiles](https://ms609.github.io/TreeSearch/articles/profile-scores.html) for Profile Parsimony\n- [Tree search with profile parsimony](https://ms609.github.io/TreeSearch/articles/profile.html)\n\n'TreeSearch' uses [semantic versioning](https://semver.org/).\nPlease note that the 'TreeSearch' project is released with a\n[Contributor Code of Conduct](CODE_OF_CONDUCT.md).\nBy contributing to this project, you agree to abide by its terms.\n\n# References\n\nBrazeau M. D., Smith M. R., Guillerme T. (2017). \n  MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability.\n  doi: [10.5281/zenodo.815372](https://doi.org/10.5281/zenodo.815372).\n\nBrazeau, M. D., Guillerme, T. and Smith, M. R. (2019).\n  An algorithm for morphological phylogenetic analysis with inapplicable data. \n  Systematic Biology, 68(4), 619-631.\n  doi: [10.1093/sysbio/syy083](https://dx.doi.org/10.1093/sysbio/syy083).\n\nFaith D. P., Trueman J. W. H. (2001).\n  Towards an inclusive philosophy for phylogenetic inference.\n  Systematic Biology, 50(3), 331–350. \n  doi: [10.1080/10635150118627](https://dx.doi.org/10.1080/10635150118627).\n\nFarris, J. S. (1969). A successive approximations approach to character weighting. \n  Systematic Biology, 18(4), 374–385.\n  doi: [10.2307/2412182](https://dx.doi.org/10.2307/2412182).\n\nGoloboff, P. A. (1993).\n  Estimating character weights during tree search.\n  Cladistics, 9(1), 83–91.\n  doi: [10.1111/j.1096-0031.1993.tb00209.x](https://doi.org/10.1111/j.1096-0031.1993.tb00209.x).\n\nGoloboff, P. A., Torres, A., Arias, J. S. (2018).\n  Weighted parsimony outperforms other methods of phylogenetic inference under \n  models appropriate for morphology.\n  Cladistics, 34(4), 407–437. doi: [10.1111/cla.12205](https://doi.org/10.1111/cla.12205).\n\nSmith, M. R. (2022a).\n  Using information theory to detect rogue taxa and improve phylogenetic trees.\n  Systematic Biology, 71(5),  1088–1094.\n  doi: [10.1093/sysbio/syab099](https://dx.doi.org/10.1093/sysbio/syab099)\n\nSmith, M. R. (2022b).\n  Robust analysis of phylogenetic tree space.\n  Systematic Biology, 71(5), 1255–1270.\n  doi: [10.1093/sysbio/syab100](https://dx.doi.org/10.1093/sysbio/syab100)\n\nSmith, M. R. (2023).\n  TreeSearch: morphological phylogenetic analysis in R.\n  R Journal, 14(4), 305-315. doi: [10.32614/RJ-2023-019](https://doi.org/10.32614/RJ-2023-019)\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftreesearch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Ftreesearch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftreesearch/lists"}