# Install mummer with Homebrew, apt Genome alignment tool. Version 4.0.1 via Homebrew; verified from local package data. ## Install ```sh sudo av install brew:mummer ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install mummer ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install mummer ``` Evidence: Debian stable package indexes: mummer from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Package facts - **Package key:** brew:mummer - **Package manager:** Homebrew - **Package manager page:** - **Version:** 4.0.1 - **Source summary:** Genome alignment tool - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** Artistic-2.0 - **Source archive:** - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - combineMUMs (cli) - delta-filter (cli) - dnadiff (cli) - exact-tandems (cli) - mummer (cli) - mummerplot (cli) - nucmer (cli) - promer (cli) - repeat-match (cli) - show-aligns (cli) - show-coords (cli) - show-diff (cli) - show-snps (cli) - show-tiling (cli) - combineMUMs (alias) - delta-filter (alias) - dnadiff (alias) - exact-tandems (alias) - mummer (alias) - mummerplot (alias) - nucmer (alias) - promer (alias) - repeat-match (alias) - show-aligns (alias) - show-coords (alias) - show-diff (alias) - show-snps (alias) - show-tiling (alias) ## Dependencies - gcc ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, sonoma, ventura, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 4.0.1 - Local data: ok - Upstream repository: https://github.com/mummer4/mummer - info: No package-manager update timestamp was available. - info: No cached GitHub release or tag data was available. ## Project history and usage MUMmer is a bioinformatics sequence-alignment package built around maximal unique matches and suffix-based data structures. The first MUMmer paper, "Alignment of whole genomes," by Arthur L. Delcher, Simon Kasif, Robert D. Fleischmann, Jeremy Peterson, Owen White, and Steven L. Salzberg, described a system for rapidly aligning genome-length DNA sequences with suffix trees, demonstrated on bacterial strains, Mycoplasma genomes, and syntenic human/mouse sequences. The name refers to MUMs, or maximal unique matches, used as anchors for large-scale alignments. ### Project history The package's major releases track the growth of genome data. MUMmer 2.1 added NUCmer and PROmer and was described by Delcher, Adam Phillippy, Jane Carlton, and Salzberg as faster and more memory-efficient for large-scale genome alignment and comparison. MUMmer 3.0, described by Stefan Kurtz, Phillippy, Delcher, and collaborators in Genome Biology, made the software open source and better suited to comparing large genomes. MUMmer4, developed by Guillaume Marcais and Aleksey Zimin with the broader MUMmer team, reworked the core from MUMmer3's 32-bit suffix tree constraints toward a 48-bit suffix-array approach and added parallel query processing; the PLOS Computational Biology paper describes MUMmer and nucmer as among the widely used alignment packages in genomics. ### How it is used In practice, researchers use the suite's commands for whole-genome alignment, draft assembly comparison, contig-to-contig alignment, variant and SNP inspection, dot plots, and translated protein-level comparisons. The package-manager niche is scientific command-line software: Homebrew and Debian/Ubuntu packages expose tools such as `mummer`, `nucmer`, `promer`, `dnadiff`, `delta-filter`, `show-coords`, `show-snps`, and `mummerplot`, making a research-grade genome comparison toolkit installable like ordinary Unix utilities. ### Sources - - - - - ## Security Notes narrow executable package without higher-risk signals. - **Geiger risk:** green / low - narrow executable package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** mummer - **Version Scheme:** 0 - **Revision:** 0 - **Conflicts With:** gd - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - mummer - 3.23+dfsg-8: normalized package name match | Debian stable package indexes: mummer from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Efficient sequence alignment of full genomes | https://mummer.sourceforge.net/ - Debian apt - mummer-doc - 3.23+dfsg-8: normalized package name match | Debian stable package indexes: mummer-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | Documentation for MUMmer | https://mummer.sourceforge.net/ - Ubuntu apt - mummer - 3.23+dfsg-8: normalized package name match | Ubuntu 24.04 LTS package indexes: mummer from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Efficient sequence alignment of full genomes | https://mummer.sourceforge.net/ - Ubuntu apt - mummer-doc - 3.23+dfsg-8: normalized package name match | Ubuntu 24.04 LTS package indexes: mummer-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | Documentation for MUMmer | https://mummer.sourceforge.net/ ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Networking and protocol packages](https://www.automicvault.com/pkg/networking-protocol-tools/) - Matched network, protocol, or remote-service metadata. - [Scientific computing packages](https://www.automicvault.com/pkg/scientific-computing-tools/) - Matched scientific computing metadata. - [gcc](https://www.automicvault.com/pkg/brew/gcc/) - Runtime dependency declared by Homebrew. - [lastz](https://www.automicvault.com/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [minimap2](https://www.automicvault.com/pkg/brew/minimap2/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [bbtools](https://www.automicvault.com/pkg/brew/bbtools/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [blast](https://www.automicvault.com/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, genomics, science, sequence-alignment. - [breseq](https://www.automicvault.com/pkg/brew/breseq/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [bwa](https://www.automicvault.com/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, dna, science, sequence-alignment. - [jellyfish](https://www.automicvault.com/pkg/brew/jellyfish/) - Shares av.db curated category or tags: bioinformatics, cli, dna, genomics, science. - [kalign](https://www.automicvault.com/pkg/brew/kalign/) - Shares av.db curated category or tags: bioinformatics, cli, dna, protein, science. - [diamond](https://www.automicvault.com/pkg/brew/diamond/) - Local package facts share a topical domain. Shared terms: alignment, bioinformatics, cli, protein, science. ## Combined YAML source View the package source record on GitHub. [combined/mummer.yml](https://github.com/automic-vault/db/blob/main/combined/mummer.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph