NGSphy, our tool for simulating NGS reads along gene trees or genome-wide along a species tree with multiple gene families, is now published in Bioinformatics.
https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty146/4925260?redirectedFrom=fulltext
Source code, full documentation, and tutorials including a “Getting started” guide are available at http://github.com/merlyescalona/ngsphy
