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

MapView is a utility script for displaying sequence alignments as provided by NUCmer or PROmer. It takes the output from show-coords or mgaps and converts it to a FIG, PDF or PS image file. By default, it produces FIG files which can be viewed with the common system utility xfig or converted to PDF or PS with the fig2dev utility (neither programs are included with MUMmer).

mapview is useful for mapping multiple query contigs (e.g. from a draft sequencing project) against an annotated reference sequence. Exons and other features can also be plotted with the NUCmer or PROmer alignments, aiding in exon refinement and analysis. Individual MUMmer hits are plotted according to their percent identity, making regions of high or low similarity easily distinguishable.

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]