Metadata-Version: 1.1
Name: CoreTracker
Version: 1.5.1
Summary: CoreTracker, A codon reassignment tracker
Home-page: https://github.com/UdeM-LBIT/CoreTracker
Author: Emmanuel Noutahi
Author-email: fmr.noutahi@umontreal.ca
License: GPL
Download-URL: https://github.com/UdeM-LBIT/CoreTracker/archive/1.5.1.tar.gz
Description: |Build Status| |PyPI version| |Anaconda-Server Badge| |Conda-Server
        Badge| 
        
        About
        ==========
        
        CoreTracker detects evidences of codon reassignment from
        the protein repertoire of a set of genomes by successively applying
        different algorithms. It’s a filtering approach that explore all
        possible reassignments in every genomes from the input set, and retain
        only the most promising one.
        
        Detailed information about the package, installation and tutorials are
        available here ==> http://udem-lbit.github.io/CoreTracker/
        
        Installation
        ============
        
        First install the dependencies which include ``gfortran``, ``PyQt4``
        ``muscle``, ``mafft`` and ``hmmer``. ``PyQt4`` also require ``Sip`` and
        ``qt``. It's easier to install those two using distribution specific
        packages.
        
        You can now download the github project and install using
        ``python setup.py install`` or pip (``pip install coretracker``).
        
        I recommend setting a virtual environment through ``virtualenv``.
        
        Alternatively, you can also install it with ``conda``, which is the
        easiest way : ``conda install -c maclandrol coretracker``.
        
        Help for installation is available at `Coretracker:
        Installation <http://udem-lbit.github.io/CoreTracker/#install>`__
        
        Basic Help
        ==========
        
        After installation, run ``coretracker -h`` for help.
        
        An example of execution is :
        
        ``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``
        
        Additional parameters can be set using the ``--params`` option. See the
        provided template
        (`param.yml <https://github.com/UdeM-LBIT/CoreTracker/blob/master/examples/test_data/param.yml>`__).
        
        Citation
        ========
        
        If you use coretracker, please cite:
        
        ::
        
            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.
        
        ::
        
            @article{noutahi2017coretracker,
              title={CoreTracker: accurate codon reassignment prediction, applied to mitochondrial genomes},
              author={Noutahi, Emmanuel and Calderon, Virginie and Blanchette, Mathieu and Lang, Franz B and El-Mabrouk, Nadia},
              journal={Bioinformatics},
              volume={33},
              number={21},
              pages={3331--3339},
              year={2017},
              publisher={Oxford University Press}
            }
        
        .. |Build Status| image:: https://travis-ci.org/UdeM-LBIT/CoreTracker.svg?branch=master
           :target: https://travis-ci.org/UdeM-LBIT/CoreTracker
        .. |PyPI version| image:: https://badge.fury.io/py/CoreTracker.svg
           :target: https://badge.fury.io/py/CoreTracker
        .. |Anaconda-Server Badge| image:: https://anaconda.org/maclandrol/coretracker/badges/version.svg
           :target: https://anaconda.org/maclandrol/coretracker
        .. |Conda-Server Badge| image:: https://anaconda.org/maclandrol/coretracker/badges/installer/conda.svg
           :target: https://conda.anaconda.org/maclandrol
        
        
Keywords: bioinformatics codon reassignment tracker
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Natural Language :: English
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License (GPL)
Classifier: Operating System :: POSIX
Classifier: Programming Language :: Python :: 2.7
