Metadata-Version: 1.1
Name: phyde
Version: 0.2.0
Summary: Hybridization detection using phylogenetic invariants
Home-page: https://github.com/pblischak/HyDe
Author: Paul Blischak & Laura Kubatko
Author-email: blischak.4@osu.edu
License: GPL
Description: 
        |Build Status| |Documentation|  |PyPI Badge|  |Gitter|
        
        HyDe: hybridization detection using phylogenetic invariants
        -----------------------------------------------------------
        
        `Read the Docs <http://hybridization-detection.rtfd.io/>`__
        -----------------------------------------------------------
        
        Installation
        ------------
        
        Requirements:
        ~~~~~~~~~~~~~
        
        -  Python 2.7
        -  Cython
        -  Numpy
        -  Scipy
        -  Pandas
        -  Matplotlib
        -  Seaborn
        -  C++ compiler (g++ >= v4.8)
        
        HyDe is a software package that detects hybridization in phylogenomic
        data sets using phylogenetic invariants. The primary interface for HyDe is a Python
        module called ``phyde`` (**P**\ ythonic **Hy**\ bridization **De**\ tection).
        ``phyde`` provides a suite of tools for performing hypothesis tests on triples of taxa
        to detect hybridization. It also has built in functions to wrap calls to the pure C++ version
        of HyDe, ``hyde_cpp``. We have provided a ``Makefile`` that
        will compile the ``hyde_cpp`` C++ executable and will then install the
        ``phyde`` Python package using the ``setup.py`` file. To ensure that the necessary
        dependencies are available, we suggest using a Python distribution such
        as `Miniconda <https://conda.io/miniconda.html>`__.
        
        .. code:: bash
        
            # To install dependencies
            pip install cython numpy scipy pandas matplotlib seaborn
        
            # Clone HyDe repository from GitHub
            git clone https://github.com/pblischak/HyDe.git
            cd HyDe
        
            # Compile hyde_cpp using `make`
            make
        
            # Now install phyde module
            python setup.py install
        
            # Test the installation
            make test
        
        The ``phyde`` module is also hosted on the Python Package Index (PyPI), and can be installed directly using
        ``pip``.
        
        .. code:: py
        
          # Install from PyPI with pip
          pip install phyde
        
        Running HyDe from the Command Line
        ----------------------------------
        
        Type ``run_hyde.py -h`` for options.
        
        .. code:: bash
        
            run_hyde.py -i <infile> -m <map-file> -o <outgroup> \
                        -n <num-ind> -t <num-taxa> -s <num-sites> \
                        --prefix <prefix>
        
        Running HyDe in Python
        ----------------------
        
        .. code:: py
        
            import phyde as hd
        
            # Run a hyde analysis
            res = hd.run_hyde("data.txt", "map.txt", "out", 16, 4, 50000, bootReps=100)
        
            # import a data set for testing particular triples
            data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 50000)
        
        .. |Build Status| image:: https://travis-ci.org/pblischak/HyDe.svg?branch=master
           :target: https://travis-ci.org/pblischak/HyDe
        
        .. |Documentation| image:: https://readthedocs.org/projects/hybridization-detection/badge/?version=latest
           :target: http://hybridization-detection.readthedocs.io/en/latest/?badge=latest
        
        .. |PyPI Badge| image:: https://badge.fury.io/py/phyde.svg
           :target: https://pypi.python.org/pypi/phyde
        
        .. |Gitter| image:: https://badges.gitter.im/Join%20Chat.svg
           :target: https://gitter.im/pblischak-HyDe/Lobby
        
Platform: UNKNOWN
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
