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        "author": "Emmanuel Noutahi",
        "author_email": "fmr.noutahi@umontreal.ca",
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        "classifiers": [
            "Development Status :: 4 - Beta",
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        "description": "|Build Status| |PyPI version| |Anaconda-Server Badge| |Conda-Server\nBadge| \n\nAbout\n==========\n\nCoreTracker detects evidences of codon reassignment from\nthe protein repertoire of a set of genomes by successively applying\ndifferent algorithms. It\u2019s a filtering approach that explore all\npossible reassignments in every genomes from the input set, and retain\nonly the most promising one.\n\nDetailed information about the package, installation and tutorials are\navailable here ==> http://udem-lbit.github.io/CoreTracker/\n\nInstallation\n============\n\nFirst install the dependencies which include ``gfortran``, ``PyQt4``\n``muscle``, ``mafft`` and ``hmmer``. ``PyQt4`` also require ``Sip`` and\n``qt``. It's easier to install those two using distribution specific\npackages.\n\nYou can now download the github project and install using\n``python setup.py install`` or pip (``pip install coretracker``).\n\nI recommend setting a virtual environment through ``virtualenv``.\n\nAlternatively, you can also install it with ``conda``, which is the\neasiest way : ``conda install -c maclandrol coretracker``.\n\nHelp for installation is available at `Coretracker:\nInstallation <http://udem-lbit.github.io/CoreTracker/#install>`__\n\nBasic Help\n==========\n\nAfter installation, run ``coretracker -h`` for help.\n\nAn example of execution is :\n\n``coretracker -t speciestree.nw -p protein.ali -n nucsequences.core --gapfilter 0.4 --iccontent 0.3  --idfilter 0.5  --norefine --wdir outdir --params param.yml``\n\nAdditional parameters can be set using the ``--params`` option. See the\nprovided template\n(`param.yml <https://github.com/UdeM-LBIT/CoreTracker/blob/master/examples/test_data/param.yml>`__).\n\nCitation\n========\n\nIf you use coretracker, please cite:\n\n::\n\n    Noutahi E, Calderon V, Blanchette M, Lang FB, El-Mabrouk N. CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes. Bioinformatics. 2017 Jun 26;33(21):3331-9.\n\n::\n\n    @article{noutahi2017coretracker,\n      title={CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes},\n      author={Noutahi, Emmanuel and Calderon, Virginie and Blanchette, Mathieu and Lang, Franz B and El-Mabrouk, Nadia},\n      journal={Bioinformatics},\n      volume={33},\n      number={21},\n      pages={3331--3339},\n      year={2017},\n      publisher={Oxford University Press}\n    }\n\n.. |Build Status| image:: https://travis-ci.org/UdeM-LBIT/CoreTracker.svg?branch=master\n   :target: https://travis-ci.org/UdeM-LBIT/CoreTracker\n.. |PyPI version| image:: https://badge.fury.io/py/CoreTracker.svg\n   :target: https://badge.fury.io/py/CoreTracker\n.. |Anaconda-Server Badge| image:: https://anaconda.org/maclandrol/coretracker/badges/version.svg\n   :target: https://anaconda.org/maclandrol/coretracker\n.. |Conda-Server Badge| image:: https://anaconda.org/maclandrol/coretracker/badges/installer/conda.svg\n   :target: https://conda.anaconda.org/maclandrol",
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