Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

A taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

(2020) Jinshui Zheng et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens

(2020) Ainsley C. Nicholson et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

(2018) Jongsik Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

Ecogenomics and Taxonomy of Cyanobacteria Phylum

(2017) Juline M. Walter et al.   Frontiers in Microbiology

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter et al.   BIOINFORMATICS

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

A Proposed Genus Boundary for the Prokaryotes Based on Genomic Insights

(2014) Q.-L. Qin et al.   JOURNAL OF BACTERIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA