Dot plot (bioinformatics): Difference between revisions

Revision as of 08:41, 28 October 2020

Revision as of 04:39, 18 December 2020

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* [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 | pages=106 |doi=10.1186/s13059-015-0670-9 |pmid=25994148 |pmc=4464727}}</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|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.