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

nucmer (NUCleotide MUMmer) is the most user-friendly alignment script for standard DNA sequence alignment. It is a robust pipeline that allows for multiple reference and multiple query sequences to be aligned in a many vs. many fashion.

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]