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.
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.
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.
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:
- Python 3.6+
- Python Modules:
- cython
- numpy
- multiprocess
- progress (optional: needed for GUI)
- C++ compiler
# 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
.
# Install from PyPI with pip
pip install phyde
Documentation for analyzing data using HyDe can be found here.