{"id":39761007,"url":"https://github.com/agormp/treetool","last_synced_at":"2026-01-18T11:37:57.158Z","repository":{"id":197742512,"uuid":"382180488","full_name":"agormp/treetool","owner":"agormp","description":"Command line program for manipulating and analyzing phylogenetic trees","archived":false,"fork":false,"pushed_at":"2024-05-27T09:45:33.000Z","size":12,"stargazers_count":0,"open_issues_count":1,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-09-09T00:58:15.125Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","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/agormp.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2021-07-01T23:34:22.000Z","updated_at":"2024-05-27T09:46:33.000Z","dependencies_parsed_at":null,"dependency_job_id":"a4b2fa41-3411-42d1-bc37-f3502cc26af1","html_url":"https://github.com/agormp/treetool","commit_stats":null,"previous_names":["agormp/treetool"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/agormp/treetool","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/agormp%2Ftreetool","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/agormp%2Ftreetool/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/agormp%2Ftreetool/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/agormp%2Ftreetool/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/agormp","download_url":"https://codeload.github.com/agormp/treetool/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/agormp%2Ftreetool/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28535169,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T10:13:46.436Z","status":"ssl_error","status_checked_at":"2026-01-18T10:13:11.045Z","response_time":98,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":[],"created_at":"2026-01-18T11:37:57.053Z","updated_at":"2026-01-18T11:37:57.136Z","avatar_url":"https://github.com/agormp.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TreeTool: python script for manipulating and analyzing phylogenetic trees\n\nCommand line tool used for data analysis in the paper \"Manual resolution of virome dark matter uncovers hundreds of viral families in the infant gut\".\n\nConverts between different phylogenetic tree file formats. Performs various manipulations and analyses on trees.\n\n## Availability\n\nThe treetool.py script is available on GitHub: https://github.com/agormp/treetool\n\n## Installation\n\nRequires installation of [phylotreelib.py](https://github.com/agormp/phylotreelib) module\n\n* Place `treetool.py` in directory that is pointed to by the PATH environment variable\n* Make script executable\n* Use on command line\n\nFor instance (on MacOS):\n```\nmv treetool.py /usr/local/bin\nchmod 755 /usr/local/bin/treetool.py\n```\n\n## Usage\n\nThe script should be run on the command line. It requires one or more tree files.\n\nThe following command prints help for command line usage:\n```\ntreetool.py -h\n```\n\nFor example, the command below reads a Newick formatted tree file, and outputs a NEXUS formatted tree file to stdout (which is then redirected to a file):\n\n```\ntreetool.py -I newick -O nexus mytreefile.newick \u003e mytreefile.nexus\n```\n\nBelow is a list of available options (output from -h option):\n\n```\nUsage: treetool.py [options] TREEFILE\n\nOptions:\n  --version             show program's version number and exit\n  -h, --help            show this help message and exit\n  -I FORMAT             Input format: nexus or newick  [default: nexus]\n  -O FORMAT             Output format: nexus or newick\n  -m, --midpoint        Root tree at midpoint\n  --root=FILE           Root tree using taxa in FILE as outgroup (one name per\n                        line)\n  --clustcut=ROOTDIST   Split leaves into clusters by cutting across tree\n                        ROOTDIST from root. Results are written to file\n                        clusterinfo.txt in dir specified using option\n                        --clustdir\n  --clustn=N            Split leaves into N clusters by cutting across tree at\n                        suitable distance from root. Results are written to\n                        file clusterinfo.txt in dir specified using option\n                        --clustdir\n  --clustrees           (Requires --clustn or clustcut): output treefiles for\n                        each cluster, and one treefile showing cluster\n                        placement\n  --clustdir=DIRNAME    Name of directory in which cluster result files are\n                        placed. [default: clusterdir]\n  --cladeinfo=FILE      For leaves listed in FILE, reports: Is this a\n                        monophyletic group? What is distance from root to\n                        enveloping clade's MRCA and MRCA's parent?\n  --rename=FILE         Rename leaves using information in FILE (format: old\n                        new)\n  --shortnames=B[,E]    Abbreviate names: Keep B first (and E last) characters\n                        in each name\n  --nameprune=SEP[,KEEP]\n                        Prune clades containing multiple taxa with identical\n                        name starts (up to first SEP). KEEP: do not prune\n                        names containing this pattern\n  --prune=FILE          Remove leaves listed in FILE (one leaf name per line)\n  --debug               Print longer error messages\n  --overwrite           Overwrite identically named previous resultfiles with\n                        no warning (e.g. for clustering options)\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fagormp%2Ftreetool","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fagormp%2Ftreetool","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fagormp%2Ftreetool/lists"}