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

To translate the coordinates referencing the concatenated reference sequences back to the individual sequences and deal with any conflict that may have arisen (i.e. a MUM that spans the boundry between two sequences). Then to extend each cluster via Smith-Waterman techniques to expand the alignment coverage. Alignments which encounter each other will be fused to form one encompasing alignment when appropriate.

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]