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* [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|last1=Rice|first1=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] {{Webarchive|url=https://web.archive.org/web/20161003142547/http://www.ac-nice.fr/svt/productions/html5/dotplot/index.htm?arn=true |date=2016-10-03 }} – 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|last1=Sonnhammer|first1=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.
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