GGDC: Genome-To-Genome Distance Calculator
The pragmatic species concept for Bacteria and Archaea is ultimately based on DNA-DNA hybridization (DDH). While enabling the taxonomist, in principle, to obtain an estimate of the overall similarity between the genomes of two strains, this technique is tedious and not easily be made reproducible between different labs and cannot be used to incrementally built up a comparative database. Recent technological progress in the area of genome sequencing calls for bioinformatics methods to replace the wet-lab DDH by in-silico genome-to-genome comparison.
The web service hosted at DSMZ offers state-of-the-art methods for inferring whole-genome distances which are well able to mimic DDH. Values calculated with GGDC yield a better correlation with wet-lab DDH values than alternative approaches such as "ANI". These distance functions can also cope with heavily reduced genomes and repetitive sequence regions. Some of them are also very robust against missing fractions of genomic information (due to incomplete genome sequencing). Thus, this web service can be used for genome-based species delineation. As of 2014 the GGDC also delineates subspecies.
Use the GGDC here.