A complete domain-to-species taxonomy for Bacteria and Archaea

Prodigal: prokaryotic gene recognition and translation initiation site identification

Doug Hyatt, Gwo-Liang Chen, Philip LoCascio et al. · BMC Bioinformatics · 2010 · 13.1K citations · Full text

Life Sciences, Bioinformatics, Microbiology +13

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

Donovan H. Parks, Michael Imelfort, Connor T. Skennerton et al. · Genome Research · 2015 · 12.8K citations · Full text

Life Sciences, Biology, Microbiology +17

Accelerated Profile HMM Searches

Sean R. Eddy · PLoS Computational Biology · 2011 · 7.5K citations · Full text

Life Sciences, Bioinformatics, Computer Science +17

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

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Life Sciences, Bioinformatics, Biology +17

Shifting the genomic gold standard for the prokaryotic species definition

Michael Richter, Ramon Rosselló‐Móra · Proceedings of the National Academy of Sciences · 2009 · 6.3K citations · Full text

Life Sciences, Biology, Microbiology +13