Editing DNA–DNA hybridization (section)

== Replacement by genome sequencing ==
{{primary sources|section|date=June 2019}}
Critics argue that the technique is inaccurate for comparison of closely related species, as any attempt to measure differences between [[orthologous]] sequences between organisms is overwhelmed by the hybridization of [[paralogous]] sequences within an organism's genome.<ref>{{cite web|author = Marks, Jonathan | title = DNA hybridization in the apes—Technical issues | url=http://personal.uncc.edu/jmarks/DNAHYB/Dnahyb2.html | date=2007-05-09 | access-date = 2019-06-02 | archive-url = https://web.archive.org/web/20070509132131/http://personal.uncc.edu/jmarks/DNAHYB/Dnahyb2.html | archive-date = 2007-05-09 }}</ref>{{better source needed|date=June 2019}}{{better source needed|date=June 2019}} [[DNA sequencing]] and computational comparisons of sequences is now generally the method for determining genetic distance, although the technique is still used in microbiology to help identify bacteria.<ref>{{cite journal| title=Use of checkerboard DNA–DNA hybridization to study complex microbial ecosystems| author=S.S. Socransky| author2=A.D. Haffajee| author3=C. Smith| author4=L. Martin| author5=J.A. Haffajee| author6=N.G. Uzel| author7=J. M. Goodson| journal=Oral Microbiology and Immunology| year=2004| volume=19| issue=6| pages=352–362| doi=10.1111/j.1399-302x.2004.00168.x| pmid=15491460}}</ref>

===''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>