mummer ☆

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Description:
Genome alignment tool

Type: Formula | Tracked Since: Dec 28, 2025

Links: Homepage | formulae.brew.sh

Category: Other

Tags: bioinformatics genomics alignment genome-comparison sequence-analysis

Install: brew install mummer

About:
MUMmer is a system for rapidly aligning entire genomes. It can find all alignments between two sets of DNA or protein sequences, reporting those that are above a chosen identity threshold. Its main value is in comparing microbial or smaller eukaryotic genomes to identify SNPs, rearrangements, and large-scale structural differences.

Key Features:

Fast alignment of whole-genome sequences
Detects SNPs, indels, and structural rearrangements
Supports both DNA and protein alignments
Extensive post-processing and visualization scripts

Use Cases:

Comparing bacterial genomes to identify mutations
Analyzing structural variations between related strains
Scaffolding and validating de novo assemblies

Alternatives:

minimap2 – Versatile long-read aligner; faster for large genomes but less specialized for whole-genome dotplots
BLAST – General-purpose sequence search; better for homology queries but not optimized for whole-genome alignments

Version History

Detected	Version	Rev	Change	Commit
Sep 16, 2025 5:24am		0	VERSION_BUMP	8209eacc