https://github.com/pblischak/hyde
Hybridization detection using phylogenetic invariants
https://github.com/pblischak/hyde
cython hybridization phylogenetic-networks phylogenomics python-package
Last synced: 12 months ago
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Hybridization detection using phylogenetic invariants
- Host: GitHub
- URL: https://github.com/pblischak/hyde
- Owner: pblischak
- License: mit
- Created: 2017-02-28T14:16:17.000Z (about 9 years ago)
- Default Branch: main
- Last Pushed: 2024-10-29T02:09:13.000Z (over 1 year ago)
- Last Synced: 2025-03-30T17:11:12.507Z (12 months ago)
- Topics: cython, hybridization, phylogenetic-networks, phylogenomics, python-package
- Language: Python
- Homepage: http://hybridization-detection.readthedocs.io
- Size: 2.03 MB
- Stars: 46
- Watchers: 2
- Forks: 14
- Open Issues: 20
-
Metadata Files:
- Readme: README.rst
- Changelog: CHANGELOG.md
- License: LICENSE
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