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* [http://cube.univie.ac.at/gepard Gepard]<ref>{{Cite journal|last1=Krumsiek|first1=Jan|last2=Arnold|first2=Roland|last3=Rattei|first3=Thomas|date=2007-04-15|title=Gepard: a rapid and sensitive tool for creating dotplots on genome scale|journal=Bioinformatics|language=en|volume=23|issue=8|pages=1026–1028|doi=10.1093/bioinformatics/btm039|pmid=17309896|issn=1367-4803|doi-access=free}}</ref> – Dot plot tool suitable for even genome scale.
* [http://sourceforge.net/projects/genomdiff Genomdiff] – An open source Java dot plot program for viruses.
* [http://last.cbrc.jp/ LAST] for whole-genome "split-alignment".<ref>{{Cite journal |author=Frith MC. and Kawaguchi R. |title=Split-alignment of genomes finds orthologies more accurately. |journal=Genome Biol. |volume=16 |year=2015 |issue=1 | pages=106 |doi=10.1186/s13059-015-0670-9 |pmid=25994148 |pmc=4464727 |doi-access=free }}</ref>
* [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|___location=Pennsylvania}}</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.
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