Mummer finds and outputs the positions and length of all sufficiently long maximal matches of a substring in query file (e.g. contigs file) and reference file (e.g. reference genome)
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.