Data from: HyDe: a Python package for genome-scale hybridization detection

The analysis of hybridization and gene flow among closely related taxa is
a common goal for researchers studying speciation and phylogeography. Many
methods for hybridization detection use simple site pattern frequencies
from observed genomic data and compare them to null models that predict an
absence of gene flow. The theory underlying the detection of hybridization
using these site pattern probabilities exploits the relationship between
the coalescent process for gene trees within population trees and the
process of mutation along the branches of the gene trees. For certain
models, site patterns are predicted to occur in equal frequency (i.e.,
their difference is 0), producing a set of functions called
textit{phylogenetic invariants}. In this paper we introduce HyDe, a
software package for detecting hybridization using phylogenetic invariants
arising under the coalescent model with hybridization. HyDe is written in
Python, and can be used interactively or through the command line using
pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as
well as on two empirical data sets from the literature. We focus in
particular on identifying individual hybrids within population samples and
on distinguishing between hybrid speciation and gene flow. HyDe is freely
available as an open source Python package under the GNU GPL v3 on both
GitHub (https://github.com/pblischak/HyDe) and the Python Package Index
(PyPI: https://pypi.python.org/pypi/phyde).