Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. - Thomas Huber; Geoffrey J. Faulkner; Philip Hugenholtz (Bioinform., 2004)

SNP-VISTA: An interactive SNP visualization tool. - Nameeta Y. Shah; Michael V. Teplitsky; Simon Minovitsky; Len A. Pennacchio; Philip Hugenholtz; Bernd Hamann; Inna Dubchak (BMC Bioinform., 2005)

An experimental metagenome data management and analysis system. - Victor M. Markowitz; Natalia Ivanova; Krishna Palaniappan; Ernest Szeto; Frank Korzeniewski; Athanasios Lykidis; Iain Anderson; Konstantinos Mavrommatis; Victor Kunin; Héctor García Martín; Inna Dubchak; Philip Hugenholtz; et al. (ISMB (Supplement of Bioinformatics), 2006)

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)

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide. - Konstantinos Liolios; Nektarios Tavernarakis; Philip Hugenholtz; Nikos Kyrpides (Nucleic Acids Res., 2006)

The integrated microbial genomes (IMG) system. - Victor M. Markowitz; Frank Korzeniewski; Krishna Palaniappan; Ernest Szeto; Greg Werner; Anu Padki; Xueling Zhao; Inna Dubchak; Philip Hugenholtz; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2006)

CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. - Charles Bland; Teresa L. Ramsey; Fareedah Sabree; Micheal Lowe; Kyndall Brown; Nikos Kyrpides; Philip Hugenholtz (BMC Bioinform., 2007)

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)

Annotation of metagenome short reads using proxygenes. - Daniel Dalevi; Natalia Ivanova; Konstantinos Mavrommatis; Sean D. Hooper; Ernest Szeto; Philip Hugenholtz; Nikos Kyrpides; Victor M. Markowitz (ECCB, 2008)

IMG/M: a data management and analysis system for metagenomes. - Victor M. Markowitz; Natalia Ivanova; Ernest Szeto; Krishna Palaniappan; Ken Chu; Daniel Dalevi; I-Min A. Chen; Yuri Grechkin; Inna Dubchak; Iain Anderson; Athanasios Lykidis; Konstantinos Mavrommatis; et al. (Nucleic Acids Res., 2008)

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes. - Erik Kristiansson; Philip Hugenholtz; Daniel Dalevi (Bioinform., 2009)

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. - Konstantinos Liolios; I-Min A. Chen; Konstantinos Mavrommatis; Nektarios Tavernarakis; Philip Hugenholtz; Victor M. Markowitz; Nikos Kyrpides (Nucleic Acids Res., 2010)

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)

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

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. - Pierre-Alain Chaumeil; Aaron J. Mussig; Philip Hugenholtz; Donovan H. Parks (Bioinform., 2020)

GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. - Donovan H. Parks; Maria Chuvochina; Christian Rinke; Aaron J. Mussig; Pierre-Alain Chaumeil; Philip Hugenholtz (Nucleic Acids Res., 2022)

GTDB-Tk v2: memory friendly classification with the genome taxonomy database. - Pierre-Alain Chaumeil; Aaron J. Mussig; Philip Hugenholtz; Donovan H. Parks (Bioinform., 2022)