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* [http://www.csb.yale.edu/userguides/graphics/whatif/html/chap13.html ANACON] – Contact analysis of dot plots.
*[http://dgenies.toulouse.inra.fr/ D-Genies]<ref>{{Cite journal|title=D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way|lastlast1=Klopp|firstfirst1=Christophe|last2=Cabanettes|first2=Floréal|journal=PeerJ|date=2018-02-23|volume=6|pages=e4958|language=en|doi=10.7287/peerj.preprints.26567v1|pmid=29888139|pmc=5991294|doi-access=free}}</ref> – Specializes in interactive whole genome dotplots of large genomes
* [http://myhits.isb-sib.ch/cgi-bin/dotlet Dotlet] – Provides a program allowing you to construct a dot plot with your own sequences.
* [http://www.bioinformatics.nl/cgi-bin/emboss/dotmatcher dotmatcher]<ref>{{Cite journal|lastlast1=Rice|firstfirst1=P.|last2=Longden|first2=I.|last3=Bleasby|first3=A.|date=June 2000|title=EMBOSS: the European Molecular Biology Open Software Suite|journal=Trends in Genetics|volume=16|issue=6|pages=276–277|issn=0168-9525|pmid=10827456|doi=10.1016/s0168-9525(00)02024-2}}</ref> – Web tool to generate dot plots (and part of the EMBOSS suite).
* [http://www.ac-nice.fr/svt/productions/html5/dotplot/index.htm?arn=true Dotplot] – easy (educational) HTML5 tool to generate dot plots from RNA sequences.
* [https://github.com/evolvedmicrobe/dotplot dotplot] – R package to rapidly generate dot plots as either traditional or ggplot graphics.
* [http://sonnhammer.sbc.su.se/Dotter.html Dotter]<ref>{{Cite journal|lastlast1=Sonnhammer|firstfirst1=E. L.|last2=Durbin|first2=R.|date=1995-12-29|title=A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis|journal=Gene|volume=167|issue=1–2|pages=GC1–10|issn=0378-1119|pmid=8566757|doi=10.1016/0378-1119(95)00714-8}}</ref> – Stand alone program to generate dot plots.
*[https://4virology.net/virology-ca-tools/jdotter/ JDotter]<ref>{{Cite journal|lastlast1=Brodie|firstfirst1=Ryan|last2=Roper|first2=Rachel L.|last3=Upton|first3=Chris|date=2004-01-22|title=JDotter: a Java interface to multiple dotplots generated by dotter|journal=Bioinformatics|language=en|volume=20|issue=2|pages=279–281|doi=10.1093/bioinformatics/btg406|pmid=14734323|issn=1367-4803|doi-access=free}}</ref> – Java version of Dotter.
* [https://github.com/molbio-dresden/flexidot Flexidot]<ref>{{Cite journal|lastlast1=Seibt|firstfirst1=Kathrin M.|last2=Schmidt|first2=Thomas|last3=Heitkam|first3=Tony|title=FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses|journal=Bioinformatics|volume=34|issue=20|pages=3575–3577|language=en|doi=10.1093/bioinformatics/bty395|pmid=29762645|date=2018-10-15|doi-access=free}}</ref> – Customizable and ambiguity-aware dotplot suite for aesthetics, batch analyses and printing (implemented in Python).
* [http://cube.univie.ac.at/gepard Gepard]<ref>{{Cite journal|lastlast1=Krumsiek|firstfirst1=Jan|last2=Arnold|first2=Roland|last3=Rattei|first3=Thomas|date=2007-04-15|title=Gepard: a rapid and sensitive tool for creating dotplots on genome scale|journal=Bioinformatics|language=en|volume=23|issue=8|pages=1026–1028|doi=10.1093/bioinformatics/btm039|pmid=17309896|issn=1367-4803|doi-access=free}}</ref> – Dot plot tool suitable for even genome scale.
* [http://sourceforge.net/projects/genomdiff Genomdiff] – An open source Java dot plot program for viruses.
* [http://last.cbrc.jp/ LAST] for whole-genome "split-alignment"<ref>{{Cite journal |author=Frith MC. and Kawaguchi R. |title=Split-alignment of genomes finds orthologies more accurately. |journal=Genome Biol. |volume=16 |year=2015 | pages=106 |doi=10.1186/s13059-015-0670-9 |pmid=25994148 |pmc=4464727}}</ref>.
==References==
<references>
<ref name="gibbs-mcintyre">{{cite journal|firstfirst1=Adrian J.|lastlast1=Gibbs|first2=George A.|last2=McIntyre|title=The Diagram, a Method for Comparing Sequences. Its Use with Amino Acid and Nucleotide Sequences|journal=Eur. J. Biochem.|volume=16|issue=1|year=1970|pages=1–11|doi=10.1111/j.1432-1033.1970.tb01046.x|pmid=5456129}}</ref>
</references>
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