Run-mummer3 is a tool for the general alignment of two sequences. This follows the same three steps of NUCmer and PROmer, in that this match, cluster and extend, however this handle any input sequence, not just nucleotide. Nevertheless, 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 and 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. Still, run-mummer3 provides few advantages of the more user friendly nucmer program, and should be avoided where possible.
Parent program: MUMmer
MUMmer or 'Maximal Unique Matches' is a bioinformatics software system for sequence alignment. It is based on the suffix tree data structure and is one of the fastest and most efficient systems available for this task, enabling it to be applied to very long sequences. It has been widely used for comparing different genomes to one another. In recent years it has become a popular algorithm for comparing genome assemblies to one another, which allows scientists to determine how a genome has changed after adding more DNA sequence or after running a different genome assembly program.