Hybridization detection using phylogenetic invariants
HyDe: hybridization detection using phylogenetic invariants
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.
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 2.7 or 3.6
- Python Modules:
- 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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