mummer
Run mummer between two sequences
base name for all generated files
Set the distance an alignment extension will attempt to extend poor scoring regions before giving up (default 200)
genome center - used in the AGP file
GFF source field
linker sequence for the merged output sequence
use all matching fragments (max) or only unique matchers (mum)
plot an alternative visualization where mummer does not attempt to put the sequences in the correct order
Organism name - used in the AGP file
Taxonomy id - used in the AGP file