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

Input is a single multi-FASTA sequence file on the command line. The command line switch '-r' specifies that the input is the reference sequence. Output is to stdout, and consists of each sequence in the input translated into all six reading frames. All the translations for a particular sequence are appended together and each seperated by a masking character.

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]