Metadata-Version: 1.0
Name: phyde
Version: 0.1.0
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|
        
        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 preferred)
        
        HyDe is a Python package that wraps a primary C++ program for running a
        hybridization detection analysis. We have provided a ``Makefile`` that
        will compile the C++ executable (``hyde_cpp``) and will then install the
        HyDe 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 HyDe Python package
            python setup.py install
        
            # Test the installation
            make test
        
        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 hyde as hd
        
            # Run a hyde analysis
            hd.run_hyde(...)
        
            # import a data set for testing particular triples
            data = hd.HydeData("data.txt", "map.txt", "out", 16, 4, 250000)
        
        .. |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
        
Platform: UNKNOWN
