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* [http://bioinfo.cristal.univ-lille.fr/yass/index.php yass]<ref>{{Cite journal |author=Noe L., Kucherov. G.|title=YASS: enhancing the sensitivity of DNA similarity search |journal=Nucleic Acids Research |volume=33|issue=2 |pages=W540–W543 |year=2005 |doi=10.1093/nar/gki478 |pmid=15980530 |pmc=1160238}}</ref> - Web-based tool to generate (both forward and reverse complement) dot plots from genomic alignments.
* [https://cran.r-project.org/web/packages/seqinr/index.html seqinr] – R package to generate dot plots.
* [https://genomevolution.org/coge/SynMap.pl SynMap] – An easy to use, web-based tool to generate dotplots for many species with access to an extensive genome database. Offered by the [[comparative genomics]] platform CoGe.
* [https://web.archive.org/web/20160416103836/https://ugene.unipro.ru/wiki/display/UUOUM15/Dotplot UGENE Dot Plot viewer] – Opensource dot plot visualizer.
* [http://www.code10.info/index.php?option=com_content&view=category&id=52&Itemid=76 General introduction to dot plots with example algorithms] and a [http://www.code10.info/index.php?view=article&catid=50%3Acat_coding_software_serolis&id=63%3Aserolis-software-package-for-dot-plot-creation&option=com_content&Itemid=61 software tool to create small and medium size dot plots.]
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