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HyDe is a software package that detects hybridization in phylogenomic data sets using phylogenetic invariants. and link to official site.
HyDe provides a number of python scripts that can be found under the Analyzing Data with HyDe section.
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[]$ run_hyde_mp.py --help
usage: run_hyde_mp.py [-h] -i -m -o -n -t -s [-j] [-tr] [-p]
[--prefix] [-q] [--ignore_amb_sites]
Options for run_hyde.py
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additional arguments:
-j, --threads number of threads [default=all available]
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GUI
HyDe also provides a GUI which can be used from an Interactive Desktop session, started via SouthPass. Within a terminal, once the module has been loaded, run the hyde_gui.py script.