OVERVIEW
mummer
MUMmer is a system for rapidly aligning DNA and protein sequences. The nucmer aligner in the current version (release 4.x) can align two mammalian genomes in about 3 hours on a typical 32+ core workstation with 64+Gb RAM; smaller genomes such as bacteria or small eukaryotes are aligned in seconds or minutes.
mummer offcial site: https://github.com/mummer4/mummer