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HyDe: Hybridization Detection Using Phylogenetic Invariants

Publication:

Blischak, P. D., J. Chifman, A. D. Wolfe, and L. S. Kubatko. 2018. HyDe: A Python Package For Genome-Scale Hybridization Detection. Systematic Biology, doi: https://doi.org/10.1093/sysbio/syy023 <https://doi.org/10.1093/sysbio/syy023>__.

Read the Docs <https://hybridization-detection.rtfd.io/>__

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. To ensure that the necessary dependencies for phyde are available, we suggest using a Python distribution such as Miniconda <https://conda.io/miniconda.html>__.

To facilitate analyses using the Python module, three scripts are provided to conduct hybridization detection analyses directly from the command line:

• run_hyde.py: runs a standard hybridization detection analysis on all triples in all directions. Results are also filtered based on whether there is significant evidence for hybridization.
• individual_hyde.py: tests each individual within a putative hybrid population using a list of specified triples specified.
• bootstrap_hyde.py: conducts bootstrap resampling of the individuals within the putative hybrid lineages for each specified triple.

These last two scripts need to be given a three column table of triples (P1, Hybrid, P2) that you wish to test:

.. code::

sp1 sp2 sp3 sp1 sp3 sp4 sp3 sp4 sp5 . . .

You can also use a results file from a previous analysis as a triples file. For example, you can use the filtered results from the run_hyde.py script so that you only run analyses on triples that have significant levels of hybridization. If you only have a few hypotheses that you want to test, then you can also pass a triples file to run_hyde.py and it will only test those hypotheses rather than testing everything.

Multithreaded versions of these scripts are also available (run_hyde_mp.py, individual_hyde_mp.py, and bootstrap_hyde_mp.py). Make sure you have the multiprocess module installed before you use them.

Graphical User Interface (Beta)

We have also developed a graphical user interface (GUI) for single-threaded hybridization detection analyses with HyDe. Users can supply file names and other options in the GUI window and hit Run or <Return> to run analyses.

.. image:: docs/img/gui.png :align: center

Getting Help

If you have questions about running HyDe, please feel free to use the gitter chatroom to get help:

|Gitter|

If you have a problem while running HyDe and you think it may be a bug, please consider filing an issue:

|HyDe Issues|

Installation

Requirements:

-  Python 3.6+
-  Python Modules:

   -  cython
   -  numpy
   -  multiprocess
   -  progress (optional: needed for GUI)

-  C++ compiler

.. code:: bash

    # To install dependencies -- add 'progress' if you're using the GUI
    pip install cython numpy multiprocess

    # Clone HyDe repository from GitHub
    git clone https://github.com/pblischak/HyDe.git
    cd HyDe

    # Now install phyde module
    python setup.py install

    # Test the installation
    make test

    # Test multithreaded scripts
    make test_threads

The ``phyde`` module is also hosted on the Python Package Index (PyPI), and can be installed directly using
``pip``.

.. code:: bash

  # Install from PyPI with pip
  pip install phyde

Documentation for analyzing data using HyDe can be found `here <http://hybridization-detection.readthedocs.io/analyze.html>`_.

.. |Build Status| image:: https://travis-ci.org/pblischak/HyDe.svg?branch=master
   :target: https://travis-ci.org/pblischak/HyDe

.. |Documentation| image:: http://readthedocs.org/projects/hybridization-detection/badge/?version=latest
   :target: http://hybridization-detection.readthedocs.io

.. |PyPI Badge| image:: https://img.shields.io/pypi/v/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

.. |HyDe Issues| image:: https://img.shields.io/badge/HyDe-Issues-blue.svg
   :target: https://github.com/pblischak/HyDe/issues