CombineMUMs combines MUMs (i.e. matches that are unique in both the reference genome and query file with contigs) in a gapfile by extending matches off ends and between MUMs. Reference sequence file is a fasta file of the reference sequence. MatchSequences is a multi-fasta file of the sequences matched against the reference
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.