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* [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.
* [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.
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