{"id":13737786,"url":"https://github.com/etetoolkit/ete","last_synced_at":"2025-04-29T23:41:24.359Z","repository":{"id":1179200,"uuid":"1077612","full_name":"etetoolkit/ete","owner":"etetoolkit","description":"Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree. ","archived":false,"fork":false,"pushed_at":"2025-04-27T10:59:46.000Z","size":132616,"stargazers_count":822,"open_issues_count":234,"forks_count":217,"subscribers_count":34,"default_branch":"ete4","last_synced_at":"2025-04-27T11:43:14.197Z","etag":null,"topics":["phylogenetics","phylogenomic","python","tree-structure","treeview","visualization"],"latest_commit_sha":null,"homepage":"http://etetoolkit.org","language":"Python","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/etetoolkit.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":".github/FUNDING.yml","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":null,"zenodo":null},"funding":{"github":["jhcepas"],"patreon":null,"open_collective":null,"ko_fi":null,"tidelift":null,"community_bridge":null,"liberapay":null,"issuehunt":null,"otechie":null,"custom":null}},"created_at":"2010-11-13T16:04:25.000Z","updated_at":"2025-04-27T10:58:21.000Z","dependencies_parsed_at":"2024-01-12T18:39:32.059Z","dependency_job_id":"dd863443-da25-41b8-84cc-9fd6261f6d55","html_url":"https://github.com/etetoolkit/ete","commit_stats":{"total_commits":3566,"total_committers":62,"mean_commits":"57.516129032258064","dds":0.5092540661805944,"last_synced_commit":"a88743b094db59b8ef0ae4cbdac53f92b5d32aa2"},"previous_names":[],"tags_count":63,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/etetoolkit%2Fete","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/etetoolkit%2Fete/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/etetoolkit%2Fete/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/etetoolkit%2Fete/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/etetoolkit","download_url":"https://codeload.github.com/etetoolkit/ete/tar.gz/refs/heads/ete4","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251134453,"owners_count":21541373,"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":["phylogenetics","phylogenomic","python","tree-structure","treeview","visualization"],"created_at":"2024-08-03T03:02:00.826Z","updated_at":"2025-04-29T23:41:24.338Z","avatar_url":"https://github.com/etetoolkit.png","language":"Python","readme":"[![](https://travis-ci.org/etetoolkit/ete.svg?branch=ete4)](https://travis-ci.org/etetoolkit/ete)\n[![Join the chat at https://gitter.im/jhcepas/ete](https://badges.gitter.im/Join%20Chat.svg)](https://gitter.im/jhcepas/ete?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n![](https://coveralls.io/repos/jhcepas/ete/badge.png)\n[![](http://img.shields.io/badge/stackoverflow-etetoolkit-blue.svg)](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete4)\n[![](http://img.shields.io/badge/biostars-etetoolkit-purple.svg)](https://www.biostars.org/t/etetoolkit,ete,ete2,ete3,ete4/)\n[![](https://img.shields.io/badge/Contributor%20Covenant-2.0-4baaaa.svg)](CODE_OF_CONDUCT.md)\n\n\n# Overview\n\nETE (Environment for Tree Exploration) is a toolkit that assists in\nthe automated manipulation, analysis and visualization of trees. It is\nmainly written in Python, and includes many extra functionalities for\nphylogenetic trees.\n\nIts main features include:\n\n- Read and write support for trees in Newick format\n- Multiple functions for traversing, searching and manipulating tree topologies and node annotations\n- Integration with NCBI Taxonomic database\n- Integration with GTDB database\n- Programmatic visualization framework\n- Visualization of huge trees based on adaptive zooming\n- Comparing trees\n- Phylogenetic functions\n  - orthology detection\n  - phylogenetic distance\n- Command line tools\n  - phylogenetic reconstruction protocols\n  - tree comparison\n  - tree diff\n\nThe official website of ETE is http://etetoolkit.org. You can find\ndownloading instructions and further documentation there.\n\nIf you use ETE, please cite:\n\n    Jaime Huerta-Cepas, François Serra and Peer Bork. \"ETE 3: Reconstruction,\n    analysis and visualization of phylogenomic data.\"  Mol Biol Evol (2016) doi:\n    10.1093/molbev/msw046\n\n\n# Installation\n\n## Quick way\n\n```sh\npip install https://github.com/etetoolkit/ete/archive/ete4.zip\n```\n\n\n## For local development\n\nTo install ETE in a local directory to help with the development, you can:\n\n- Clone this repository (`git clone https://github.com/etetoolkit/ete.git`)\n- Install dependecies\n  - If you are using [conda](https://conda.io/):\n  `conda install -c conda-forge cython bottle brotli numpy scipy`\n  - Otherwise, you can install them with `pip install \u003cdependencies\u003e`\n- Build and install ete4 from the repository's root directory: `pip install -e .`\n\n## Optional dependencies\n\nIf you want to use the `treeview` module (which depends on\n[PyQt](https://www.riverbankcomputing.com/software/pyqt/)), you can\nadd `[treeview]` to the pip installation.\n\nFor example with `pip install -e .[treeview]` for a local editable\ninstallation. Or `pip install -e .[treeview,test,doc,render_sm]` to\nalso include the modules for testing, generating the documentation,\nand smartview file rendering.\n\n\n# Exploring a tree\n\nTo simply load a tree from a file (`my_tree.nw`) and start exploring\nit interactively, you can use the `ete4` utility and run:\n\n```sh\nete4 explore -t my_tree.nw\n```\n\nOr start a python session and write:\n\n```py\nfrom ete4 import Tree\n\nt = Tree(open('my_tree.nw'))\n\nt.explore()\n```\n\nIt will open a browser window with an interface to explore the tree.\n\n\n# Documentation\n\nMost documentation is automatically generated with\n[sphinx](https://www.sphinx-doc.org) from the contents of the `doc`\ndirectory, and is available at https://etetoolkit.github.io/ete/ .\n\n\n# Gallery of examples\n\n![](https://raw.githubusercontent.com/etetoolkit/ete/ete4/doc/images/gallery.png)\n\n\n# Getting support\n\nRather than sending direct support-related emails to the developers,\nit is better to keep the communication public.\n\nFor question on how to use ETE in the bioinformatics context, use\n[Biostars](http://biostars.org) with the `etetoolkit` tag, or [stack\noverflow](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete4).\n\n[![](http://img.shields.io/badge/biostars-etetoolkit-purple.svg)](https://www.biostars.org/post/search/?query=etetoolkit+or+ete+or+ete2+or+ete3+or+ete4)\n[![](http://img.shields.io/badge/stackoverflow-etetoolkit-blue.svg)](https://stackoverflow.com/questions/tagged/etetoolkit+or+ete3+or+ete4)\n\nFor bug reports, feature requests and general discussion, use\nhttps://github.com/etetoolkit/ete/issues\n\nFor more technical problems, you can also use the official ETE mailing\nlist at https://groups.google.com/d/forum/etetoolkit. To avoid spam,\nmessages from new users are moderated. Expect some delay until your\nfirst message appears after your account is validated.\n\nFor any other inquiries (collaborations, sponsoring, etc), please\ncontact jhcepas@gmail.com.\n\n\n# Tests\n\nYou can launch some tests by running:\n\n```sh\n./run_tests.py\n```\n\n\n# Contributing and bug reporting\n\nhttps://github.com/etetoolkit/ete/wiki/Contributing\n\n\n# Roadmap\n\nhttps://github.com/etetoolkit/ete/wiki/ROADMAP\n","funding_links":["https://github.com/sponsors/jhcepas"],"categories":["Python"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fetetoolkit%2Fete","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fetetoolkit%2Fete","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fetetoolkit%2Fete/lists"}