{"id":15444420,"url":"https://github.com/jlsteenwyk/clipkit","last_synced_at":"2026-02-27T20:30:19.288Z","repository":{"id":40389475,"uuid":"254887970","full_name":"JLSteenwyk/ClipKIT","owner":"JLSteenwyk","description":"a multiple sequence alignment-trimming algorithm for accurate phylogenomic 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align=\"center\"\u003e\n  \u003ca href=\"https://github.com/jlsteenwyk/clipkit\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/JLSteenwyk/ClipKIT/master/docs/_static/img/logo.jpg\" alt=\"Logo\" width=\"400\"\u003e\n  \u003c/a\u003e\n  \u003cp align=\"center\"\u003e\n    \u003ca href=\"https://jlsteenwyk.com/ClipKIT/\"\u003eDocs\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/clipkit/issues\"\u003eReport Bug\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/clipkit/issues\"\u003eRequest Feature\u003c/a\u003e\n  \u003c/p\u003e\n    \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://github.com/JLSteenwyk/ClipKIT/actions\" alt=\"Build\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JLSteenwyk/ClipKIT/ci.yml?branch=master\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://codecov.io/gh/jlsteenwyk/clipkit\" alt=\"Coverage\"\u003e\n          \u003cimg src=\"https://codecov.io/gh/jlsteenwyk/clipkit/branch/master/graph/badge.svg?token=0J49I6441V\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://github.com/JLSteenwyk/ClipKIT/graphs/contributors\" alt=\"Contributors\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/contributors/JLSteenwyk/ClipKIT\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://bsky.app/profile/jlsteenwyk.bsky.social\" target=\"_blank\" rel=\"noopener noreferrer\"\u003e\n          \u003cimg src=\"https://img.shields.io/badge/Bluesky-0285FF?logo=bluesky\u0026logoColor=fff\"\u003e\n        \u003c/a\u003e\n        \u003cbr /\u003e\n        \u003ca href=\"https://pepy.tech/badge/clipkit\"\u003e\n          \u003cimg src=\"https://static.pepy.tech/personalized-badge/clipkit?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=PyPi%20Downloads\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://anaconda.org/bioconda/clipkit\"\u003e\n          \u003cimg src=\"https://img.shields.io/conda/dn/bioconda/clipkit?label=bioconda%20downloads\" alt=\"Bioconda Downloads\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://lbesson.mit-license.org/\" alt=\"License\"\u003e\n            \u003cimg src=\"https://img.shields.io/badge/License-MIT-blue.svg\"\u003e\n        \u003c/a\u003e\n        \u003cbr /\u003e\n        \u003ca href=\"https://pypi.org/project/clipkit/\" alt=\"PyPI - Python Version\"\u003e\n            \u003cimg src=\"https://img.shields.io/pypi/pyversions/clipkit\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3001007\"\u003e\n          \u003cimg src=\"https://zenodo.org/badge/DOI/10.1371/journal.pbio.3001007.svg\"\u003e  \n        \u003c/a\u003e   \n    \u003c/p\u003e\n\u003c/p\u003e\n\n\n\u003ccenter\u003e\u003ch2\u003eRun \u003ca href=\"https://clipkit.genomelybio.com/\"\u003eClipKIT in the browser\u003c/a\u003e and leave the computing up to \u003ca href=\"https://www.genomelybio.com/\"\u003eus\u003c/a\u003e!\u003c/h2\u003e\u003c/center\u003e\n\u003cbr /\u003e\n\nClipKIT is a fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others.\u003cbr /\u003e\u003cbr /\u003e\nIf you found ClipKIT useful, please cite *ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference*. Steenwyk et al. 2020, PLOS Biology. doi: [10.1371/journal.pbio.3001007](https://jlsteenwyk.com/publication_pdfs/2020_Steenwyk_etal_PLOS_Biology.pdf).\n\n\u003cbr /\u003e\u003cbr /\u003e\n\n---\n\n\u003cbr /\u003e\n\nThis documentation covers downloading and installing ClipKIT. Details about each function as well as tutorials for using ClipKIT are available in the [online documentation](https://jlsteenwyk.com/ClipKIT/).\nRelease automation details are documented in [RELEASE.md](RELEASE.md).\n\n\u003cbr /\u003e\n\n**Quick Start**\n\n```shell\n# install\npip install clipkit\n# run\nclipkit input.fa\n```\n\n**eComp archives**\n\nClipKIT can trim Evolutionary Compression (`.ecomp`) archives directly. Simply\npass the `.ecomp` file to the CLI, and ClipKIT will unpack its metadata sidecar\nand native payload before trimming the alignment. Archives encoded with zstd\nrequire the optional [`zstandard`](https://pypi.org/project/zstandard/) module;\nall other payload encodings work out of the box. By default the trimmed\nalignment is written back as an `.ecomp` archive (with a gzip fallback payload);\nspecify `-of fasta` if you prefer a text format.\n\n\u003cbr /\u003e\n\n**Installation**\n\n**If you are having trouble installing ClipKIT, please contact the lead developer, Jacob L. Steenwyk, via [email](https://jlsteenwyk.com/contact.html) or [twitter](https://twitter.com/jlsteenwyk) to get help.**\n\nTo install using *pip*, we strongly recommend building a virtual environment to avoid software dependency issues. To do so, execute the following commands:\n```shell\n# create virtual environment\npython -m venv venv\n# activate virtual environment\nsource venv/bin/activate\n# install clipkit\npip install clipkit\n```\n**Note: the virtual environment must be activated to use *clipkit*.**\n\nAfter using ClipKIT, you may wish to deactivate your virtual environment and can do so using the following command:\n```shell\n# deactivate virtual environment\ndeactivate\n```\n\n\u003cbr /\u003e\n\nSimilarly, to install from source, we strongly recommend using a virtual environment. To do so, use the following commands:\n```shell\n# download\ngit clone https://github.com/JLSteenwyk/ClipKIT.git\ncd ClipKIT/\n# create virtual environment\npython -m venv venv\n# activate virtual environment\nsource venv/bin/activate\n# install\nmake install\n```\nTo deactivate your virtual environment, use the following command:\n```shell\n# deactivate virtual environment\ndeactivate\n```\n**Note: the virtual environment must be activated to use *clipkit*.**\n\n\u003cbr /\u003e\n\nTo install via anaconda, execute the following command:\n\n``` shell\nconda install bioconda::clipkit\n```\nVisit here for more information: https://anaconda.org/bioconda/clipkit\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fclipkit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjlsteenwyk%2Fclipkit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fclipkit/lists"}