Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S rDNA. - T. Z. DeSantis Jr.; I. Dubosarskiy; S. R. Murray; Gary L. Andersen (Bioinform., 2003)

NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. - Todd Z. DeSantis; Philip Hugenholtz; Keith Keller; Eoin L. Brodie; Niels Larsen; Yvette M. Piceno; Richard Phan; Gary L. Andersen (Nucleic Acids Res., 2006)

Automated group assignment in large phylogenetic trees using GRUNT: GRouping, Ungrouping, Naming Tool. - Daniel Dalevi; Todd Z. DeSantis; Jakob Fredslund; Gary L. Andersen; Victor M. Markowitz; Philip Hugenholtz (BMC Bioinform., 2007)

PyNAST: a flexible tool for aligning sequences to a template alignment. - J. Gregory Caporaso; Kyle Bittinger; Frederic D. Bushman; Todd Z. DeSantis; Gary L. Andersen; Rob Knight 001 (Bioinform., 2010)