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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
* [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|last=Rice|first=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}}</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|last=Sonnhammer|first=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=
* [http://virology.uvic.ca/virology-ca-tools/jdotter/ JDotter]<ref>{{Cite journal|last=Brodie|first=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|url=https://academic.oup.com/bioinformatics/article/20/2/279/204948|journal=Bioinformatics|language=en|volume=20|issue=2|pages=279–281|doi=10.1093/bioinformatics/btg406|issn=1367-4803}}</ref> – Java version of Dotter.
* [https://github.com/molbio-dresden/flexidot Flexidot]<ref>{{Cite journal|last=Seibt|first=Kathrin M.|last2=Schmidt|first2=Thomas|last3=Heitkam|first3=Tony|title=FlexiDot: Highly customizable, ambiguity-aware dotplots for visual sequence analyses|url=https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty395/4995848|journal=Bioinformatics|volume=34|issue=20|pages=3575–3577|language=en|doi=10.1093/bioinformatics/bty395|pmid=29762645|date=2018-10-15}}</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|last=Krumsiek|first=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|url=https://academic.oup.com/bioinformatics/article/23/8/1026/198110|journal=Bioinformatics|language=en|volume=23|issue=8|pages=1026–1028|doi=10.1093/bioinformatics/btm039|pmid=17309896|issn=1367-4803}}</ref> – Dot plot tool suitable for even genome scale.
* [http://sourceforge.net/projects/genomdiff Genomdiff] – An open source Java dot plot program for viruses.
* [https://www.bx.psu.edu/~rsharris/lastz/ lastz]<ref>{{Cite book|title=Improved pairwise alignment of genomic DNA. Ph.D. thesis.|last=Harris|first=R. S.|publisher=The Pennsylvania State University|year=2007|isbn=|___location=Pennsylvania|pages=}}</ref> and [http://globin.bx.psu.edu/dist/laj/ laj] – Programs to prepare and visualize genomic alignments.
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==References==
<references>
<ref name="gibbs-mcintyre">{{cite journal|first=Adrian J.|last=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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