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*[http://dgenies.toulouse.inra.fr/ D-Genies]<ref>{{Cite journal|title=D-GENIES : Dot plot large GENomes in an interactive, efficient and simple way|last=Klopp|first=Christophe|last2=Cabanettes|first2=Floréal|date=2018-02-23|language=en|doi=10.7287/peerj.preprints.26567v1}}</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|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|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|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=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|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).
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