Increased sequencing of microbial genomes has revealed that prevailing prokaryotic
species assignments can be inconsistent with whole genome information for a significant
number of species. The long-standing need for a systematic and scalable species
assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI)
metric, which is widely acknowledged as a robust measure of genomic relatedness. In this
work, we demonstrate that the combination of gANI and the alignment fraction (AF) between …

Species assignments in prokaryotes use a manual, poly-phasic approach utilizing both
phenotypic traits and sequence information of phylogenetic marker genes. With thousands
of genomes being sequenced every year, an automated, uniform and scalable approach
exploiting the rich genomic information in whole genome sequences is desired, at least for
the initial assignment of species to an organism. We have evaluated pairwise genome-wide
Average Nucleotide Identity (gANI) values and alignment fractions (AFs) for nearly 13,000 …