Promer generates amino acid alignments between two mutli-FASTA DNA input files. The out.delta output file lists the distance between insertions and deletions that produce maximal scoring alignments between each sequence. The show-* utilities know how to read this format. The DNA input is translated into all 6 reading frames in order to generate the output, but the output coordinates reference the original DNA input. What is delta file? The delta file is a representation of the all-vs-all alignment between the sequences contained in the multi-FASTA input files. It catalogs the coordinates of aligned regions and the distance between insertions and deletions contained in these alignment regions.
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.