HyDe

1 Overview | 2 Using | 2.1 Multicore | 2.2 GUI

Overview

HyDe is a software package that detects hybridization in phylogenomic data sets using phylogenetic invariants.
- HyDe provides a number of python scripts that can be found under the Analyzing Data with HyDe section.

Using

Use the module name hyde to discover versions available and to load the application.

HyDe appears to be a number of python scripts that are called:

Multicore

A number of the scripts provide multi core functionality. Please review each script to see what is does/doesn’t provide. For example:

[]$ 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
...
additional arguments:
  -j, --threads    number of threads [default=all available]
...

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.