decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisiveness. - Ilya Y. Zhbannikov; Joseph W. Brown; James A. Foster (BCB, 2013)

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)

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs. - Stephen A. Smith; Joseph W. Brown; Cody E. Hinchliff (PLoS Comput. Biol., 2013)

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees. - Matthew W. Pennell; Jonathan M. Eastman; Graham J. Slater; Joseph W. Brown; Josef C. Uyeda; Richard G. FitzJohn; Michael E. Alfaro; Luke J. Harmon (Bioinform., 2014)

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)

FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool. - Joseph W. Brown; Meg Pirrung; Lee Ann McCue (Bioinform., 2017)

Phyx: phylogenetic tools for unix. - Joseph W. Brown; Joseph F. Walker; Stephen A. Smith (Bioinform., 2017)

Verbalizing phylogenomic conflict: Representation of node congruence across competing reconstructions of the neoavian explosion. - Nico M. Franz; Lukas J. Musher; Joseph W. Brown; Shizhuo Yu; Bertram Ludäscher (PLoS Comput. Biol., 2019)