{"id":24182994,"url":"https://github.com/ms609/treetools","last_synced_at":"2025-05-08T23:43:36.672Z","repository":{"id":35662156,"uuid":"215972277","full_name":"ms609/TreeTools","owner":"ms609","description":"Create, modify and analyse phylogenetic trees in R","archived":false,"fork":false,"pushed_at":"2025-05-05T11:17:04.000Z","size":19420,"stargazers_count":23,"open_issues_count":16,"forks_count":7,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-05-08T23:43:24.983Z","etag":null,"topics":["cran","evolutionary-biology","phylogenetic-trees","phylogenetics","r-package"],"latest_commit_sha":null,"homepage":"https://ms609.github.io/TreeTools/","language":"R","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":"2019-10-18T08:02:40.000Z","updated_at":"2025-05-01T06:05:28.000Z","dependencies_parsed_at":"2023-02-14T08:31:58.087Z","dependency_job_id":"a9944eb1-d5e7-4ccf-b619-7168ba890d2a","html_url":"https://github.com/ms609/TreeTools","commit_stats":{"total_commits":969,"total_committers":6,"mean_commits":161.5,"dds":0.4158926728586171,"last_synced_commit":"dd1a77cd34b36e47fd824cf86460c6636967dd7b"},"previous_names":[],"tags_count":44,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeTools","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeTools/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeTools/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ms609%2FTreeTools/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ms609","download_url":"https://codeload.github.com/ms609/TreeTools/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253166474,"owners_count":21864467,"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","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":["cran","evolutionary-biology","phylogenetic-trees","phylogenetics","r-package"],"created_at":"2025-01-13T08:45:56.510Z","updated_at":"2025-05-08T23:43:36.653Z","avatar_url":"https://github.com/ms609.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TreeTools\n\n[![codecov](https://codecov.io/gh/ms609/TreeTools/branch/master/graph/badge.svg)](https://codecov.io/gh/ms609/TreeTools)\n[![CRAN Status Badge](https://www.r-pkg.org/badges/version/TreeTools)](https://cran.r-project.org/package=TreeTools)\n[![CRAN Downloads](https://cranlogs.r-pkg.org/badges/TreeTools)](https://ms609.github.io/usage/#treetools)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3522726.svg)](https://doi.org/10.5281/zenodo.3522725)\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.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n\n'TreeTools' is an R package that provides efficient implementations of \nfunctions for the creation, modification and analysis of phylogenetic trees.\n\nApplications include:\ngeneration of trees with specified shapes;\nanalysis of tree shape;\nrooting of trees and extraction of subtrees;\ncalculation and depiction of node support;\ncalculation of ancestor-descendant relationships;\nimport and export of trees from Newick, Nexus and \n[TNT](https://www.lillo.org.ar/phylogeny/tnt/) formats;\nand analysis of partitions and cladistic information.\n\nIt complements packages such as \n['ape'](https://cran.r-project.org/package=ape),\n['phangorn'](https://cran.r-project.org/package=phangorn) and\n['phytools'](https://cran.r-project.org/package=phytools),\naiming for efficient and robust implementations of functions, typically\napplied to unweighted trees (i.e. those without edge lengths).\n\n# Installation\n\nInstall and load the library from CRAN as follows:\n```r\ninstall.packages(\"TreeTools\")\nlibrary(\"TreeTools\")\n```\n\nInstall the very latest version, which may be under development, with:\n```r\nif (!require(\"devtools\")) install.packages(\"devtools\")\ndevtools::install_github(\"ms609/TreeTools\")\n```\n\nPlease note that the 'TreeTools' 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","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftreetools","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fms609%2Ftreetools","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fms609%2Ftreetools/lists"}