ATLAS (Automatic Tool for Local Assembly Structures) - a comprehensive infrastructure for assembly, annotation, and genomic binning of metagenomic and metatranscriptomic data. - Richard Allen White III; Joseph Brown; Sean Colby; Christopher C. Overall; Joon-Yong Lee; Jeremy Zucker; Kurt R. Glaesemann; Christer Jansson; Janet K. Jansson (PeerJ Prepr., 2017)

MerCat: a versatile k-mer counter and diversity estimator for database-independent property analysis obtained from metagenomic and/or metatranscriptomic sequencing data. - Richard Allen White III; Ajay Panyala; Kevin Glass; Sean Colby; Kurt R. Glaesemann; Christer Jansson; Janet K. Jansson (PeerJ Prepr., 2017)

efam: an expanded, metaproteome-supported HMM profile database of viral protein families. - Ahmed A. Zayed; Dominik Lücking; Mohamed Mohssen; Dylan Cronin; Ben Bolduc; Ann C. Gregory; Katherine R. Hargreaves; Paul D. Piehowski; Richard Allen White III; Eric L. Huang; Joshua N. Adkins; Simon Roux; et al. (Bioinform., 2021)

MetaCerberus: distributed highly parallelized HMM-based processing for robust functional annotation across the tree of life. - Jose L. Figueroa III; Eliza Dhungel; Madeline Bellanger; Cory R. Brouwer; Richard Allen White III (Bioinform., 2024)