Phylocom: software for the analysis of phylogenetic community structure and trait evolution. - Campbell O. Webb; David D. Ackerly; Steven W. Kembel (Bioinform., 2008)

Picante: R tools for integrating phylogenies and ecology. - Steven W. Kembel; Peter D. Cowan; Matthew R. Helmus; William K. Cornwell; Hélène Morlon; David D. Ackerly; Simon P. Blomberg; Campbell O. Webb (Bioinform., 2010)

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data. - Thomas J. Sharpton; Samantha J. Riesenfeld; Steven W. Kembel; Joshua Ladau; James P. O'Dwyer; Jessica L. Green; Jonathan A. Eisen; Katherine S. Pollard (PLoS Comput. Biol., 2011)

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance. - Steven W. Kembel; Martin Wu; Jonathan A. Eisen; Jessica L. Green (PLoS Comput. Biol., 2012)

Phylogenetic Diversity Theory Sheds Light on the Structure of Microbial Communities. - James P. O'Dwyer; Steven W. Kembel; Jessica L. Green (PLoS Comput. Biol., 2012)

Estimating metacommunity extent using data on species abundances, environmental variation, and phylogenetic relationships across geographic space. - Brian A. Maurer; Steven W. Kembel; Andrew J. Rominger; Brian J. McGill (Ecol. Informatics, 2013)

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks. - Henry Xing; Steven W. Kembel; Vladimir Makarenkov (Bioinform., 2020)