All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy

Genome-informed Bradyrhizobium taxonomy: where to from here?

(2019) Juanita R. Avontuur et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

(2018) Seong-In Na et al.   JOURNAL OF MICROBIOLOGY

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

(2018) Donovan H Parks et al.   NATURE BIOTECHNOLOGY

Whole Genome Analyses Suggests that Burkholderia sensu lato Contains Two Additional Novel Genera (Mycetohabitans gen. nov., and Trinickia gen. nov.): Implications for the Evolution of Diazotrophy and Nodulation in the Burkholderiaceae

(2018) Paulina Estrada-de los Santos et al.   Genes

Prokaryotic species are sui generis evolutionary units

(2018) Marike Palmer et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy

(2016) Vladimir Novichkov et al.   BIOINFORMATICS

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

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

Draft genome sequences of Pantoea agglomerans and Pantoea vagans isolates associated with termites

(2016) Marike Palmer et al.   Standards in Genomic Sciences

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

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

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

Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation

(2013) Christopher J Grim et al.   BMC GENOMICS

Microbial genomic taxonomy

(2013) Cristiane C Thompson et al.   BMC GENOMICS

Advantages and limitations of genomics in prokaryotic taxonomy

(2013) E. Sentausa et al.   CLINICAL MICROBIOLOGY AND INFECTION

PSimScan: Algorithm and Utility for Fast Protein Similarity Search

(2013) Anna Kaznadzey et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Comparative Genome Analysis of Prevotella ruminicola and Prevotella bryantii: Insights into Their Environmental Niche

(2010) Janaki Purushe et al.   MICROBIAL ECOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs

(2010) Alexander F. Auch et al.   Standards in Genomic Sciences

Bradyrhizobium pachyrhizi sp. nov. and Bradyrhizobium jicamae sp. nov., isolated from effective nodules of Pachyrhizus erosus

(2009) M. H. Ramirez-Bahena et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

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

A Genomic Distance Based on MUM Indicates Discontinuity between Most Bacterial Species and Genera

(2008) M. Deloger et al.   JOURNAL OF BACTERIOLOGY