mummerplot is a part of the MUMmer package, for the rapid alignment of very large DNA and amino acid sequences.

mummerplot is a script utility that takes output from mummer, nucmer, promer or show-tiling, and converts it to a format suitable for plotting with gnuplot. In addition to producing the plot data, mummerplot also generates a gnuplot script that will generate the graph. Since mummerplot simple generates gnuplot input, gnuplot must also be installed.

References:
Delcher AL, Kasif S, Fleischmann RD, Peterson J, White O, Salzberg SL: Alignment of whole genomes, Nucleic Acids Res. 1999 Jun 1;27(11):2369-76.[Entrez]

Delcher AL, Phillippy A, Carlton J, Salzberg SL: Fast algorithms for large-scale genome alignment and comparison, Nucleic Acids Res. 2002 Jun 1;30(11):2478-83.[Entrez]

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL: Versatile and open software for comparing large genomes, Genome Biol. 2004;5(2):R12. Epub 2004 Jan 30.[Entrez]