MUMmer allows you to rapidly align entire prokaryote genomes or eukaryote chromosomes.  It consists of nineteen scripts that perform different types of genome alignment analyses.

Using MUMmer on HPC

MUMmer uses a suffix tree strategy to enable the alignment of genome sized segments very quickly. The complete MUMmer user manual and a tutorial is available at SourceForge. Input sequences need to be in FastA format. Launch each script by typing its name in lower case, e.g:

nucmer E.coli.fsa H.pylori.fsa

See the documentation for all of the script names and uses.