phyde 1.0.1

Hybridization Detection Using Phylogenetic Invariants

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 (Pythonic Hybridization Detection). 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:

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.

Getting Help

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

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

Installation

Requirements:

• Python 3.9+

• Python Modules:

  • cython

  • numpy

  • multiprocess

  • progress (optional: needed for GUI)

• C++ compiler

# 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.

# Install from PyPI with pip
pip install phyde

Documentation for analyzing data using HyDe can be found here.