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href=\"https://github.com/jlsteenwyk/phykit\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/JLSteenwyk/PhyKIT/master/docs/_static/img/phykit_logo.png\" alt=\"Logo\" width=\"400\"\u003e\n  \u003c/a\u003e\n  \u003cp align=\"center\"\u003e\n    \u003ca href=\"https://jlsteenwyk.com/PhyKIT/\"\u003eDocs\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/phykit/issues\"\u003eReport Bug\u003c/a\u003e\n    ·\n    \u003ca href=\"https://github.com/jlsteenwyk/phykit/issues\"\u003eRequest Feature\u003c/a\u003e\n  \u003c/p\u003e\n    \u003cp align=\"center\"\u003e\n        \u003ca href=\"https://github.com/JLSteenwyk/PhyKIT/actions\" alt=\"Build\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/actions/workflow/status/JLSteenwyk/PhyKIT/ci.yml?branch=master\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://codecov.io/gh/jlsteenwyk/phykit\" alt=\"Coverage\"\u003e\n          \u003cimg src=\"https://codecov.io/gh/jlsteenwyk/phykit/branch/master/graph/badge.svg?token=0J49I6441V\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://github.com/JLSteenwyk/PhyKIT/graphs/contributors\" alt=\"Contributors\"\u003e\n            \u003cimg src=\"https://img.shields.io/github/contributors/JLSteenwyk/PhyKIT\"\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/phykit\"\u003e\n          \u003cimg src=\"https://static.pepy.tech/personalized-badge/phykit?period=total\u0026units=international_system\u0026left_color=grey\u0026right_color=blue\u0026left_text=PyPi%20Downloads\"\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        \u003ca href=\"https://pypi.org/project/phykit/\" alt=\"PyPI - Python Version\"\u003e\n            \u003cimg src=\"https://img.shields.io/pypi/pyversions/phykit\"\u003e\n        \u003c/a\u003e\n        \u003ca href=\"https://academic.oup.com/bioinformatics/article-abstract/37/16/2325/6131675?redirectedFrom=fulltext\"\u003e\n          \u003cimg src=\"https://zenodo.org/badge/DOI/10.1093/bioinformatics/btab096.svg\"\u003e\n        \u003c/a\u003e\n    \u003c/p\u003e\n\u003c/p\u003e\n\nPhyKIT is a UNIX shell toolkit for processing and analyzing phylogenomic data.\u003cbr /\u003e\u003cbr /\u003e\nIf you found PhyKIT useful, please cite *PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data*. Bioinformatics. doi: [10.1093/bioinformatics/btab096](https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/btab096/6131675).\n\u003cbr /\u003e\u003cbr /\u003e\n\n---\n\nThis documentation covers downloading and installing PhyKIT. Details about each function as well as tutorials for using PhyKIT are available in the \u003ca href=\"https://jlsteenwyk.com/PhyKIT/\"\u003eonline documentation\u003c/a\u003e.\n\n\u003cbr /\u003e\n\n**Quick Start**\n\n```shell\n# install\npip install phykit\n# run\nphykit \u003cfunction\u003e \u003cinput file\u003e\n```\n\n\u003cbr /\u003e\n\n**Installation** \u003cbr /\u003e\n\n**If you are having trouble installing PhyKIT, 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 phykit\npip install phykit\n```\n\n**Note, the virtual environment must be activated to use phykit.**\n\nAfter using PhyKIT, 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/PhyKIT.git\ncd PhyKIT/\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 phykit.**\n\n\u003cbr /\u003e\n\nTo install via anaconda, execute the following command:\n```shell\nconda install bioconda::phykit\n```\nVisit here for more information:\nhttps://anaconda.org/bioconda/phykit\n\n\u003cbr /\u003e\n\nTo test phykit installation, launch the help message\n\n```shell\nphykit -h\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fphykit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fjlsteenwyk%2Fphykit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fjlsteenwyk%2Fphykit/lists"}