Genomics, metagenomics and -omics approaches in general generate a lot of data. We needed a method to delineate genomic data relating to bacteria and we needed it to be fast, accurate and automated. We came up with specI which can group organisms into species clusters based on universal marker genes.



The exponentially increasing number of sequenced genomes necessitates fast, accurate, universally applicable and automated approaches for the delineation of prokaryotic species. We developed specI (species identification tool;, a method to group organisms into species clusters based on 40 universal, single-copy phylogenetic marker genes. Applied to 3,496 prokaryotic genomes, specI identified 1,753 species clusters. Of 314 discrepancies with a widely used taxonomic classification, >62% were resolved by literature support.


Mende DR1, Sunagawa S, Zeller G, Bork P

Journal and Citation

Nature Methods 10(9): 881-884

DOI: 10.1038/nmeth.2575


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