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        "author": "Shareef M. Dabdoub",
        "author_email": "dabdoub.2@osu.edu",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Natural Language :: English",
            "Operating System :: MacOS :: MacOS X",
            "Operating System :: Microsoft :: Windows",
            "Operating System :: POSIX :: BSD",
            "Operating System :: POSIX :: Linux",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "PhyloToAST\r\n===========\r\n.. image:: https://img.shields.io/pypi/v/phylotoast.svg?style=plastic   \r\n    :target: https://pypi.python.org/pypi/phylotoast\r\n    :alt: Latest Version\r\n.. image:: https://img.shields.io/pypi/l/phylotoast.svg?style=plastic   \r\n    :target: https://pypi.python.org/pypi/phylotoast\r\n    :alt: License\r\n.. image:: https://img.shields.io/pypi/format/phylotoast.svg?style=plastic   \r\n    :target: https://pypi.python.org/pypi/phylotoast\r\n    :alt: Download format\r\n.. image:: https://img.shields.io/travis/smdabdoub/phylotoast.svg?style=plastic\r\n    :target: https://travis-ci.org/smdabdoub/phylotoast\r\n    :alt: Travis CI build status\r\n.. image:: https://img.shields.io/badge/install%20with-bioconda-4682b4.svg?style=plastic\r\n   :target: https://bioconda.github.io/recipes/phylotoast/README.html\r\n\r\nThe PhyloToAST project is a collection of python code and scripts that\r\nmodify the QIIME [1] pipeline by adding/changing several\r\nsteps including: support for cluster-computing, multiple primer support\r\n(eliminate primer bias) [2], enhanced support for species-specific\r\nanalysis, and additional visualization tools.\r\n\r\nInstallation\r\n------------\r\n\r\nTo install PhyloToAST from PyPI:\r\n\r\n.. code-block:: bash\r\n\r\n    $ pip install phylotoast\r\n\r\nFrom source:\r\n\r\n.. code-block:: bash\r\n\r\n    $ python setup.py install\r\n\r\n\r\nDocumentation\r\n-------------\r\n\r\nFull documentation for the scripts and code is available at\r\n`docs.phylotoast.org`_ (hosted by `Read the Docs`_)\r\n\r\nRequirements\r\n------------\r\n\r\nThe list of required modules will vary depending on which executable scripts and/or\r\nparts of the API you may use. For this reason there are no required dependencies\r\nthat will be automatically installed along with PhyloToAST. Each executable script will\r\ncheck that the required libraries are installed and will print a message if any are not\r\nfound. \r\n\r\nIf you would like to install everything up front, the following is a complete list of libraries\r\nthat are used in PhyloToAST:\r\n\r\n- `numpy`_\r\n- `scipy`_\r\n- `matplotlib`_ >= 1.5.0\r\n- `biopython`_ >= 1.60 \r\n- `scikit-bio`_\r\n- `scikit-learn`_\r\n- `pandas`_\r\n- `statsmodels`_\r\n- `palettable`_\r\n- `biom-format`_ >= 2.1.5\r\n- `h5py`_ (for parsing BIOM v2.x format files)\r\n\r\nSource\r\n------\r\n\r\nThe `PhyloToAST source`_ is hosted on github.\r\n\r\nCiting\r\n------\r\n\r\nDabdoub, S. M. *et al.* PhyloToAST: Bioinformatics tools for species-level analysis and\r\nvisualization of complex microbial datasets. *Sci. Rep.* **6**, 29123; doi: 10.1038/srep29123 (2016).\r\n\r\nPublications using PhyloToAST\r\n------------------------------\r\nTsigarida and Dabdoub et al., *The Influence of Smoking on the Peri-Implant\r\nMicrobiome*. Journal of Dental Research, 2015; `doi: 10.1177/0022034515590581`_\r\n\r\nMason et al., *The subgingival microbiome of clinically healthy current\r\nand never smokers*. The ISME Journal, 2014; `doi:10.1038/ismej.2014.114`_\r\n\r\nDabdoub et al., *Patient-specific Analysis of Periodontal and Peri-implant Microbiomes*.\r\nJournal of Dental Research, 2013; `doi: 10.1177/0022034513504950`_\r\n\r\nReferences\r\n----------\r\n\r\n[1] J Gregory Caporaso, et al., *QIIME allows analysis of\r\nhigh-throughput community sequencing data*. Nature Methods, 2010;\r\n`doi:10.1038/nmeth.f.303`_\r\n\r\n[2] Kumar PS, et al., *Target Region Selection Is a Critical Determinant\r\nof Community Fingerprints Generated by 16S Pyrosequencing*. PLoS ONE\r\n(2011) 6(6): e20956. `doi:10.1371/journal.pone.0020956`_\r\n\r\n.. _docs.phylotoast.org: http://docs.phylotoast.org\r\n.. _Read the Docs: http://readthedocs.org\r\n.. _numpy: http://numpy.org\r\n.. _scipy: http://scipy.org\r\n.. _matplotlib: http://matplotlib.org\r\n.. _biopython: http://biopython.org\r\n.. _scikit-bio: http://scikit-bio.org\r\n.. _scikit-learn: http://scikit-learn.org\r\n.. _pandas: http://pandas.pydata.org\r\n.. _statsmodels: http://statsmodels.sourceforge.net/\r\n.. _palettable: https://jiffyclub.github.io/palettable/\r\n.. _biom-format: http://biom-format.org\r\n.. _h5py: http://www.h5py.org/\r\n.. _PhyloToAST source: http://github.com/smdabdoub/phylotoast\r\n.. _`doi: 10.1177/0022034515590581`: http://dx.doi.org/10.1177/0022034515590581\r\n.. _`doi:10.1038/ismej.2014.114`: http://dx.doi.org/10.1038/ismej.2014.114\r\n.. _`doi: 10.1177/0022034513504950`: http://dx.doi.org/10.1177/0022034513504950\r\n.. _`doi:10.1038/nmeth.f.303`: http://dx.doi.org/10.1038/nmeth.f.303\r\n.. _`doi:10.1371/journal.pone.0020956`: http://dx.doi.org/10.1371/journal.pone.0020956",
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