Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. - Arlin Stoltzfus; Hilmar Lapp; Naim Matasci; Helena F. Deus; Brian Sidlauskas; Christian M. Zmasek; Gaurav Vaidya; Enrico Pontelli; Karen Cranston; Rutger A. Vos; Campbell O. Webb; Luke J. Harmon; et al. (BMC Bioinform., 2013)

Phylesystem: a git-based data store for community-curated phylogenetic estimates. - Emily Jane McTavish; Cody E. Hinchliff; James F. Allman; Joseph W. Brown; Karen Cranston; Mark T. Holder; Jonathan Rees; Stephen A. Smith (Bioinform., 2015)

TreeToReads - a pipeline for simulating raw reads from phylogenies. - Emily Jane McTavish; James B. Pettengill; Steve Davis 002; Hugh Rand; Errol Strain; Marc Allard; Ruth E. Timme (BMC Bioinform., 2017)

Physcraper: a Python package for continually updated phylogenetic trees using the Open Tree of Life. - Luna L. Sánchez-Reyes; Martha Kandziora; Emily Jane McTavish (BMC Bioinform., 2021)