Strainer: software for analysis of population variation in community genomic datasets. - John M. Eppley; Gene W. Tyson; Wayne M. Getz; Jillian F. Banfield (BMC Bioinform., 2007)

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data. - Lauren M. Bragg; Glenn Stone; Margaret K. Butler; Philip Hugenholtz; Gene W. Tyson (PLoS Comput. Biol., 2013)

The Bio-Community Perl toolkit for microbial ecology. - Florent E. Angly; Christopher J. Fields; Gene W. Tyson (Bioinform., 2014)

STAMP: statistical analysis of taxonomic and functional profiles. - Donovan H. Parks; Gene W. Tyson; Philip Hugenholtz; Robert G. Beiko (Bioinform., 2014)

OrfM: a fast open reading frame predictor for metagenomic data. - Ben J. Woodcroft; Joel A. Boyd; Gene W. Tyson (Bioinform., 2016)