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Hybridization detection using phylogenetic invariants

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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.

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.

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 2.7 or 3.6
  • Python Modules:
    • Cython
    • Numpy
    • Matplotlib
    • Seaborn
    • Multiprocess
  • C++ compiler
# To install dependencies
pip install cython numpy matplotlib seaborn 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.

# Install from PyPI with pip
pip install phyde

Documentation for analyzing data using HyDe can be found here.

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