Editing DNA–DNA hybridization (section)

===''In silico'' methods===
The modern approach is to carry out DNA–DNA hybridization ''in silico'' utilizes completely or partially [[Whole genome sequencing|sequenced genomes]].<ref name="doi10.1186/1471-2105-14-60">{{cite journal|vauthors =  Meier-Kolthoff JP, Auch AF, Klenk HP, Goeker M|title=Genome sequence-based species delimitation with confidence intervals and improved distance functions|journal=BMC Bioinformatics|volume=14|pages=60|year=2013|doi=10.1186/1471-2105-14-60|pmid=23432962|pmc=3665452 |doi-access=free }}</ref> Digital DDH (dDDH) is developed at the [[DSMZ]] and uses the GBDP (Genome Blast Distance Phylogeny) algorithm to produce DDH-analogous methods. DSMZ offers several web services based on dDDH. dDDH does not suffer from DDH's issues with paralogous genes, large repeats, reduced genomes, and low-complexity regions. Among other algorithmic improvements, it solves the problem with paralogous sequences by carefully filtering them from the matches between the two genome sequences.<ref name="doi10.1186/1471-2105-14-60" />

dDDH has been used for resolving difficult taxa such as ''[[Escherichia coli]]'', ''[[Bacillus cereus]]'' group, and ''[[Aeromonas]]''.<ref>{{cite journal |last1=Riojas |first1=Marco A. |last2=McGough |first2=Katya J. |last3=Rider-Riojas |first3=Cristin J. |last4=Rastogi |first4=Nalin |last5=Hazbón |first5=Manzour Hernando |title=Phylogenomic analysis of the species of the Mycobacterium tuberculosis complex demonstrates that Mycobacterium africanum, Mycobacterium bovis, Mycobacterium caprae, Mycobacterium microti and Mycobacterium pinnipedii are later heterotypic synonyms of Mycobacterium tuberculosis |journal=International Journal of Systematic and Evolutionary Microbiology |date=1 January 2018 |volume=68 |issue=1 |pages=324–332 |doi=10.1099/ijsem.0.002507 |pmid=29205127 |doi-access=free}}</ref> The Judicial Commission of [[International Committee on Systematics of Prokaryotes]] has admitted dDDH as taxonomic evidence.<ref>{{cite journal |last1=Arahal |first1=David R. |last2=Bull |first2=Carolee T. |last3=Busse |first3=Hans-Jürgen |last4=Christensen |first4=Henrik |last5=Chuvochina |first5=Maria |last6=Dedysh |first6=Svetlana N. |last7=Fournier |first7=Pierre-Edouard |last8=Konstantinidis |first8=Konstantinos T. |last9=Parker |first9=Charles T. |last10=Rossello-Mora |first10=Ramon |last11=Ventosa |first11=Antonio |last12=Göker |first12=Markus |title=Judicial Opinions 123–127 |journal=International Journal of Systematic and Evolutionary Microbiology |date=27 April 2023 |volume=72 |issue=12 |doi=10.1099/ijsem.0.005708|pmid=36748499 |hdl=10261/295959 |hdl-access=free }}</ref>