As part of this project, pairwise average nucleotide identities (ANI) and fraction of orthologous genomic regions (Alignment fraction, AF) have been computed for nearly 28,000 bacterial and archaeal genomes. By clustering genomes based on their pairwise AF and ANI values, we were able to ascertain mis-assignment of species names in genomes spanning nearly 18% of all existing species. Additionally, the complete linkage clustering made it possible to confidently assign species to nearly 326 genomes. Through the analysis of cliques, it has also become possible to identify speciation events within existing species. Within the JGI’s production pipeline, ANI is used to ascertain the species specificity of single cells and genomes extracted from metagenomes, and also as a metric for quality control within IMG. While ANI is integrated within IMG, ani.jgi.doe.gov serves the current data.