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        "author": "Dessimoz Lab - Laboratory of Computational Evolutionary Biology and Genomics",
        "author_email": "adrian.altenhoff@inf.ethz.ch",
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        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "Environment :: Console",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "pyHam: A Tool to Analyze Hierarchical Orthologous Groups (HOGs)\n===============================================================\n\n\nMotivation\n----------\npyHam is a library to facilitate the analysis of hierarchical orthologous groups.\nIt also contains a few tools to run standard type of analysis.\n\nCurrently, Ham is limited to analyze HOGs that are stored in an orthoXML file.\nMore information on the schema of orthoxml and some examples are\navailable at http://orthoxml.org.\n\nFor extended documentation we refer to the docs folder that contain information\non common use cases and API documentation of the library.\n\nHow to cite pyHam\n-----------------\nIf you use pyHam in your work, please consider citing:\n\n*Cl\u00e9ment-Marie Train, Miguel Pignatelli, Adrian Altenhoff, Christophe Dessimoz; iHam and pyHam: visualizing and processing hierarchical orthologous groups, Bioinformatics, bty994, https://doi.org/10.1093/bioinformatics/bty994*\n\nInstallation\n------------\nHam is written in python3 (also compatible with python2), with little external dependencies, i.e.\ncurrently ete3, lml, six. The setup script should resolve these\ndependencies automatically.\nConsider using pip to install the package directly from a checked out git repo\n\n.. code-block:: sh\n\n   python -m pip install --upgrade pip\n   pip install pyham\n\nExample\n-------\nWe prepare a ready-to-use example (see example folder) with few python scripts to use main pyHam features.\nYou just have to run the following command in bash:\n\n.. code-block:: sh\n\n   python run_hog_queries.py\n   python run_treeProfile.py\n   python run_iHam.py\n\nGetting started\n---------------\nWe create a small introductory blog post about HOGs and pyHam at http://lab.dessimoz.org/blog/2017/06/29/pyham. We highly recommend you to read it before starting using pyHam.\n\nWe also create an ipython notebook to help you with basic uses of pyHam API and embedded tools at http://zoo.cs.ucl.ac.uk/tutorials/tutorial_pyHam_get_started.html.\n\nTable of compatibility\n----------------------\n\nSupport for pyHam by various HOG inference resources.\n\n+-----------------+------------------------------+---------------------------------------+-----------+\n| Resource        | Species tree format          | OrthoXML                              | SUPPORT   |\n+=================+==============================+=======================================+===========+\n||OMA browser|_   | |PhyloXMLo|_ and |Newicko|_  ||All HOGso|_ , or |one HOG at a timeo|_|    YES    |\n+-----------------+------------------------------+---------------------------------------+-----------+\n||OMA standalone|_| PhyloXML and Newick          | All HOGs                              |    YES    |\n+-----------------+------------------------------+---------------------------------------+-----------+\n| |Ensembl|_      | |Newicke|_                   |    one HOG at a time                  |    YES    |\n+-----------------+------------------------------+---------------------------------------+-----------+\n| |HieranoidDB|_  | |Newickh|_                   |    one HOG at a time                  |    YES    |\n+-----------------+------------------------------+---------------------------------------+-----------+\n\n.. |OMA browser| replace:: ``OMA browser``\n.. |OMA standalone| replace:: ``OMA standalone``\n.. |Ensembl| replace:: ``Ensembl``\n.. |HieranoidDB| replace:: ``HieranoidDB``\n\n.. |PhyloXMLo| replace:: ``PhyloXML``\n.. |Newicko| replace:: ``Newick``\n.. |PhyloXMLs| replace:: ``PhyloXML``\n.. |Newicks| replace:: ``Newick``\n.. |Newicke| replace:: ``Newick``\n.. |Newickh| replace:: ``Newick``\n\n.. |All HOGso| replace:: ``All HOGs``\n.. |one HOG at a timeo| replace:: ``one HOG at a time``\n\n.. _OMA browser: https://omabrowser.org\n.. _OMA standalone: https://omabrowser.org/standalone/\n.. _Ensembl: https://www.ensembl.org/index.html\n.. _HieranoidDB: http://hieranoidb.sbc.su.se/\n\n.. _PhyloXMLo: https://omabrowser.org/All/speciestree.phyloxml\n.. _Newicko: https://omabrowser.org/All/speciestree.nwk\n.. _Newicke: https://www.ensembl.org/info/about/speciestree.html\n.. _Newickh: http://hieranoid.sbc.su.se/download/H2/66c.tree\n\n.. _All HOGso:  https://omabrowser.org/All/oma-hogs.orthoXML.gz\n.. _one HOG at a timeo:  https://omabrowser.org/oma/hogs/\n\n\nDocumentation\n-------------\nYou can the full documentation of pyHam at http://zoo.cs.ucl.ac.uk/doc/pyham/index.html\n\n\n\n\n",
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        "keywords": "orthology, HOGs, orthoxml",
        "license": "MIT",
        "maintainer": "",
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        "name": "pyham",
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