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            "Development Status :: 5 - Production/Stable",
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            "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": "NOTICE\r\n=======\r\nThe QIIME-tools project is now obsolete and has been\r\nreplaced by `PhyloToAST`_. The new project is available on GitHub and\r\non PyPI. PhyloToAST can be installed with pip:\r\n\r\n .. code-block:: bash\r\n\r\n    $ pip install phylotoast\r\n\r\n\r\nQIIME-tools\r\n===========\r\n.. image:: https://pypip.in/version/qiime-tools/badge.svg\r\n    :target: https://pypi.python.org/pypi/qiime-tools/\r\n    :alt: Latest Version\r\n.. image:: https://pypip.in/d/qiime-tools/badge.svg\r\n    :target: https://crate.io/packages/qiime-tools/\r\n.. image:: https://pypip.in/license/qiime-tools/badge.svg\r\n    :target: https://pypi.python.org/pypi/qiime-tools/\r\n    :alt: License\r\n.. image:: https://pypip.in/format/qiime-tools/badge.svg\r\n    :target: https://pypi.python.org/pypi/qiime-tools/\r\n    :alt: Download format\r\n\r\nThe QIIME-tools project is a collection of python code and scripts that\r\nmodify the original 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 QIIME-tools from PyPI:\r\n\r\n.. code-block:: bash\r\n\r\n    $ pip install qiime-tools\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 the\r\n`QIIME-tools documentation site`_\r\n\r\nRequirements\r\n------------\r\n\r\n`matplotlib`_ for PCoA plots. `Biopython`_ for some sequence and fastq\r\nprocessing, although its use is being phased out. `fuzzpy`_ for the\r\notu\\_calc module. Note that these are not listed as dependencies in the install\r\nscript because they are not required for all functionality. Install as needed.\r\n\r\nSource\r\n------\r\n\r\nThe `QIIME-tools source`_ is hosted on github.\r\n\r\nCiting\r\n------\r\n\r\nA manuscript describing the qiime-tools software is currently in\r\npreparation. Until publication, please cite the github repository and\r\nthe author: Shareef M. Dabdoub.\r\n\r\nPublications using QIIME-tools\r\n------------------------------\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.. _PhyloToAST: https://github.com/smdabdoub/phylotoast\r\n.. _QIIME-tools documentation site: http://qiime-tools.readthedocs.org\r\n.. _matplotlib: http://matplotlib.org\r\n.. _Biopython: http://biopython.org\r\n.. _fuzzpy: http://mavrinac.com/index.cgi?page=fuzzpy\r\n.. _QIIME-tools source: http://github.com/smdabdoub/qiime-tools\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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