References

After All, Only Millions?

10.1128/mbio.00999-16 · 2016 · External reference

Multiple comparative metagenomics using multisetk-mer counting

10.7717/peerj-cs.94 · 2016 · External reference

A User's Guide to a Data Base of the Diversity of Pseudomonas syringae and Its Application to Classifying Strains in This Phylogenetic Complex

10.1371/journal.pone.0105547 · 2014 · External reference

Why do species vary in their rate of molecular evolution?

10.1098/rsbl.2009.0136 · 2009 · External reference

Kmer-db: instant evolutionary distance estimation

10.1093/bioinformatics/bty610 · 2019 · External reference

Phenetic Comparison of Prokaryotic Genomes Using k-mers

10.1093/molbev/msx200 · 2017 · External reference

Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex

10.1371/journal.pone.0150183 · 2016 · External reference

A New Genomics-Driven Taxonomy of Bacteria and Archaea: Are We There Yet?

10.1128/jcm.00200-16 · 2016 · External reference

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

10.3389/fmicb.2017.02422 · 2017 · External reference

Phylogenomics and systematics in Pseudomonas

10.3389/fmicb.2015.00214 · 2015 · External reference

DNA–DNA hybridization values and their relationship to whole-genome sequence similarities

10.1099/ijs.0.64483-0 · 2007 · External reference

Use of DNA reassociation in bacterial classification

10.1139/m88-092 · 1988 · External reference

Genome‐based evolutionary history of Pseudomonas spp

10.1111/1462-2920.14130 · 2018 · External reference

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

10.1038/s41467-018-07641-9 · 2018 · External reference

Centrifuge: rapid and sensitive classification of metagenomic sequences

10.1101/gr.210641.116 · 2016 · External reference

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

10.1099/ijsem.0.000760 · 2016 · External reference

Scaling laws predict global microbial diversity

10.1073/pnas.1521291113 · 2016 · External reference

Genome sequence-based species delimitation with confidence intervals and improved distance functions

10.1186/1471-2105-14-60 · 2013 · External reference

RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification

10.1186/s13059-018-1554-6 · 2018 · External reference

Mash: fast genome and metagenome distance estimation using MinHash

10.1186/s13059-016-0997-x · 2016 · External reference

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

10.1186/s12864-015-1419-2 · 2015 · External reference

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

10.1038/nbt.4229 · 2018 · External reference

LPSN – List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on

10.1099/ijsem.0.002786 · 2018 · External reference

Historical evolution and current status of the taxonomy of genus Pseudomonas

10.1016/j.meegid.2009.08.001 · 2009 · External reference

The current status on the taxonomy of Pseudomonas revisited: An update

10.1016/j.meegid.2017.10.026 · 2018 · External reference

Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens

10.1039/c5ay02550h · 2016 · External reference

Shifting the genomic gold standard for the prokaryotic species definition

10.1073/pnas.0906412106 · 2009 · External reference

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

10.1093/nar/gky467 · 2018 · External reference

Past and future species definitions for Bacteria and Archaea

10.1016/j.syapm.2015.02.001 · 2015 · External reference

Reflections on the introduction of the Digital Protologue Database – a partial success?

10.1007/s10482-018-01221-z · 2019 · External reference

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

10.1038/nmeth.4458 · 2017 · External reference

Functional Microbial Features Driving Community Assembly During Seed Germination and Emergence

10.3389/fpls.2018.00902 · External reference

Microbial species delineation using whole genome sequences

10.1093/nar/gkv657 · 2015 · External reference

A proposal for a portal to make earth’s microbial diversity easily accessible and searchable

10.1007/s10482-017-0849-z · 2017 · External reference

Kraken: ultrafast metagenomic sequence classification using exact alignments

10.1186/gb-2014-15-3-r46 · 2014 · External reference

A large-scale evaluation of algorithms to calculate average nucleotide identity

10.1007/s10482-017-0844-4 · 2017 · External reference