npm

mummer

Fast sequence alignment tool for whole genome comparisons

brewmacoslinux
Try with needOr install directly
Source

About

Genome alignment tool

Commands

nucmerpromerdelta-filtershow-coordsshow-alignsshow-tiling

Examples

Align two DNA sequences and generate delta file$ nucmer reference.fasta query.fasta -o alignment
Filter alignment delta file by sequence identity and length$ delta-filter -i 95 -l 1000 alignment.delta > filtered.delta
Display alignment coordinates in readable format$ show-coords -r filtered.delta