Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/pblischak/hyde

Hybridization detection using phylogenetic invariants
https://github.com/pblischak/hyde

cython hybridization phylogenetic-networks phylogenomics python-package

Last synced: 6 days ago
JSON representation

Hybridization detection using phylogenetic invariants

Awesome Lists containing this project

README 

        

|Documentation|  |PyPI Badge|



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 `__.



`Read the Docs `__

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



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 `__.



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 ```` 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 3.9+

-  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

    python3 -m pip install -r requirements.txt



    # Clone HyDe repository from GitHub

    git clone https://github.com/pblischak/HyDe.git

    cd HyDe



    # Now install phyde module

    python3 -m pip 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 `_.



.. |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