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* [http://www.csb.yale.edu/userguides/graphics/whatif/html/chap13.html ANACON] – Contact analysis of dot plots.
* [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|url=https://www.ncbi.nlm.nih.gov/pubmed/10827456|journal=Trends in
* [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.
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