run-mummer3 is a part of the MUMmer package, for the rapid alignment of very large DNA and amino acid sequences.

run-mummer3 is the simplest pipeline of the latest MUMmer3.0 programs. It runs the same matching and clustering algorithm as nucmer and promer, however it uses a different extension technique and does not perform the important pre- and post-processing steps of NUC/PROmer. Because of its simplistic form, run-mummer3 can only handle a single reference sequence, but like run-mummer1 its error-focused output makes it a handy tool for detecting SNPs and other small errors. The only major difference between run-mummer3 and run-mummer1 is the new version's ability to handle multiple query sequences and its tolerance of large rearrangements. This makes run-mummer3 well suited for error detection between highly similar sequences that may have large rearrangements, inversions etc.

Edit the script by adding the -D option to the combineMUMs command line to output a format designed for SNP identification.

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]