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"info": {
"author": "Zachary Sailer",
"author_email": "zachsailer@gmail.com",
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"License :: OSI Approved :: MIT License",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
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"description": "\n![](\"docs/_logo/banner.png\")
\n\n[](https://gitter.im/phylopandas/Lobby)\n[](http://phylopandas.readthedocs.io/en/latest/?badge=latest)\n[](https://travis-ci.org/Zsailer/phylopandas)\n[](https://mybinder.org/v2/gh/Zsailer/phylopandas/master?filepath=examples%2Fintro-notebook.ipynb)\n\n**Bringing the [Pandas](https://github.com/pandas-dev/pandas) `DataFrame` to phylogenetics.**\n\n\nPhyloPandas provides a Pandas-like interface for reading sequence and phylogenetic tree data into pandas DataFrames. This enables easy manipulation of phylogenetic data using familiar Python/Pandas functions. Finally, phylogenetics for humans!\n\n
\n\n## How does it work?\n\nDon't worry, we didn't reinvent the wheel. **PhyloPandas** is simply a [DataFrame](https://github.com/pandas-dev/pandas)\n(great for human-accessible data storage) interface on top of [Biopython](https://github.com/biopython/biopython) (great for parsing/writing sequence data) and [DendroPy](https://github.com/jeetsukumaran/DendroPy) (great for reading tree data).\n\nPhyloPandas does two things:\n1. It offers new `read` functions to read sequence/tree data directly into a DataFrame.\n2. It attaches a new `phylo` **accessor** to the Pandas DataFrame. This accessor provides writing methods for sequencing/tree data (powered by Biopython and dendropy).\n\n## Basic Usage\n\n**Sequence data:**\n\nRead in a sequence file.\n```python\nimport phylopandas as ph\n\ndf1 = ph.read_fasta('sequences.fasta')\ndf2 = ph.read_phylip('sequences.phy')\n```\n\nWrite to various sequence file formats.\n\n```python\ndf1.phylo.to_clustal('sequences.clustal')\n```\n\nConvert between formats.\n\n```python\n# Read a format.\ndf = ph.read_fasta('sequences.fasta')\n\n# Write to a different format.\ndf.phylo.to_phylip('sequences.phy')\n```\n\n**Tree data:**\n\nRead newick tree data\n```python\ndf = ph.read_newick('tree.newick')\n```\n\nVisualize the phylogenetic data (powered by [phylovega](https://github.com/Zsailer/phylovega)).\n```python\ndf.phylo.display(\n height=500,\n)\n```\n\n
\n\n## Contributing\n\nIf you have ideas for the project, please share them on the project's [Gitter chat](https://gitter.im/phylopandas/Lobby).\n\nIt's *easy* to create new read/write functions and methods for PhyloPandas. If you\nhave a format you'd like to add, please submit PRs! There are many more formats\nin Biopython that I haven't had the time to add myself, so please don't be afraid\nto add them! I thank you ahead of time!\n\n## Testing\n\nPhyloPandas includes a small [pytest](https://docs.pytest.org/en/latest/) suite. Run these tests from base directory.\n```\n$ cd phylopandas\n$ pytest\n```\n\n## Install\n\nInstall from PyPI:\n```\npip install phylopandas\n```\n\nInstall from source:\n```\ngit clone https://github.com/Zsailer/phylopandas\ncd phylopandas\npip install -e .\n```\n\n## Dependencies\n\n- [BioPython](https://github.com/biopython/biopython): Library for managing and manipulating biological data.\n- [DendroPy](https://github.com/jeetsukumaran/DendroPy): Library for phylogenetic scripting, simulation, data processing and manipulation\n- [Pandas](https://github.com/pandas-dev/pandas): Flexible and powerful data analysis / manipulation library for Python\n- [pandas_flavor](https://github.com/Zsailer/pandas_flavor): Flavor pandas objects with new accessors using pandas' new register API (with backwards compatibility).\n\n\n",
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