Metadata-Version: 1.1
Name: OrthoEvol
Version: 0.9.0a2
Summary: This package aids in the analysis of orthologous genes.
Home-page: https://github.com/datasnakes/OrthoEvolution
Author: Rob Gilmore & Shaurita Hutchins
Author-email: datasnakes@gmail.com
License: MIT
Description-Content-Type: UNKNOWN
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        OrthoEvolution

        ====================

        OrthoEvolution is an **easy to use** and comprehensive python package which aids in the **analysis and

        visualization of comparative evolutionary genetics** related projects such as the **inference of orthologs**.

        

        Overview

        --------------------------

        This package focuses on **inferring orthologs** using NCBI's blast, various sequence alignment strategies,

        and phylogenetics analyses including PAML, PhyML, ete3, and more tools.

        

        Ultimately, the goal of this project is to create a **reusable pipeline** for the

        inference of orthologs in order to ensure reproducibility of data as well as improve

        the management and analysis of (what can be) large datasets.  The Cookies, Manager, Pipeline,

        and Tools modules act as a framework for our workflow, while the Orthologs

        module provides access to specific functions for our various ortholog inference projects.

        

        View our `read the docs <http://datasnakes-scripts.readthedocs.io/en/master/>`__ and feel free to also

        read `this related paper <https://www.frontiersin.org/articles/10.3389/fnhum.2014.00283/full>`__ to gain

        more insight into this project/python package.

        

        

        Installation

        ----------------

        View the below methiods for installing this package. Python3.5 and higher is required.

        

        PyPi

        ~~~~~~~~~~~~~~~~

        ``pip install OrthoEvol``

        

        GitHub

        ~~~~~~~~~~~~~~~~

        1. Download the zip file and unzip it or ``git clone https://github.com/datasnakes/OrthoEvolution.git``

        2. ``cd OrthoEvolution``

        3. ``pip install .``

        

        Development Code

        ~~~~~~~~~~~~~~~~

        **WARNING** : This code is actively under development and may not be reliable.  Please create an `issue <https://github.com/datasnakes/OrthoEvolution/issues>`_ for questions about development.

        

        1. Download the zip file and unzip it or ``git clone -b dev-master https://github.com/datasnakes/OrthoEvolution.git``

        2. ``cd OrthoEvolution``

        3. ``pip install .``

        

        Examples

        ----------------

        Check out this `tutorial <https://github.com/datasnakes/OrthoEvolution/wiki/Tutorial>`__ in our Wiki Docs.

        

        .. code:: python

        

            import OrthoEvol

        

        Tests

        ----------------

        To run tests, type ``nosetests Tests/`` in the OrthoEvolution directory.

        

        Contributors

        ----------------

        This package was created by the Datasnakes.

        

        -  Rob Gilmore \| Github: `@grabear <https://github.com/grabear>`__ \|

           `✉ <mailto:robgilmore127@gmail.com>`__

        -  Shaurita Hutchins \| Github:

           `@sdhutchins <https://github.com/sdhutchins>`__ \|

           `✉ <mailto:sdhutchins@outlook.com>`__

        

        If you would like to contribute to this package, install the package in development mode,

        and check out our `contributing guidelines <https://github.com/datasnakes/OrthoEvolution/blob/master/CONTRIBUTING.rst>`__.

        

        

        Citations

        ----------------

        We're so thankful to have a resource such as

        `Biopython <http://biopython.org/wiki/Biopython>`__. They inspired this

        package.

        

        *Cock, P.J.A. et al. Biopython: freely available Python tools for

        computational molecular biology and bioinformatics. Bioinformatics 2009

        Jun 1; 25(11) 1422-3 http://dx.doi.org/10.1093/bioinformatics/btp163

        pmid:19304878*

        

        License

        ----------------

        `MIT <https://github.com/datasnakes/OrthoEvolution/blob/master/LICENSE>`_

        
Keywords: bioinformatics science evolution orthology psychiatry genetics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: Unix
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Framework :: Flask
Classifier: Framework :: R-Shiny
Classifier: Framework :: Cookiecutter
