macOS
Homebrewverified · 100%
brew install mummerlocal Homebrew formula metadata
brew / rank 7309
Install mummer with Homebrew, apt
Genome alignment tool. Version 4.0.1 via Homebrew; verified from local package data. Also installable with debian: sudo apt install mummer.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install mummerDebian stable package indexes · mummer · source: deb.debian.org
overview
Package summary
Genome alignment tool
Project links
Commands and aliases
- combineMUMs
- delta-filter
- dnadiff
- exact-tandems
- mummer
- mummerplot
- nucmer
- promer
- repeat-match
- show-aligns
- show-coords
- show-diff
- show-snps
- show-tiling
history
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 posture
Risk level: green
narrow executable package without higher-risk signals.
Risk classifier
green risk · low confidence · appliance
Why
- narrow executable package without higher-risk signals
Signals
- metadata:no-higher-risk-signals
Install behavior
- No Homebrew bottle metadata was recorded.
Recommended review
Before unattended agent use, check whether the tool reads plaintext credentials, writes remote state, publishes artifacts, or shells out to plugins.
executables
Installed executables
| Command | Kind | Exposure | Note |
|---|---|---|---|
combineMUMs | executable | indexed executable | Discovered from the local executable index. |
delta-filter | executable | indexed executable | Discovered from the local executable index. |
dnadiff | executable | indexed executable | Discovered from the local executable index. |
exact-tandems | executable | indexed executable | Discovered from the local executable index. |
mummer | executable | indexed executable | Discovered from the local executable index. |
mummerplot | executable | indexed executable | Discovered from the local executable index. |
nucmer | executable | indexed executable | Discovered from the local executable index. |
promer | executable | indexed executable | Discovered from the local executable index. |
repeat-match | executable | indexed executable | Discovered from the local executable index. |
show-aligns | executable | indexed executable | Discovered from the local executable index. |
show-coords | executable | indexed executable | Discovered from the local executable index. |
show-diff | executable | indexed executable | Discovered from the local executable index. |
show-snps | executable | indexed executable | Discovered from the local executable index. |
show-tiling | executable | indexed executable | Discovered from the local executable index. |
freshness
Version and freshness
These signals separate page generation age, package-manager activity, and upstream release comparison. Version lag is warned only when an evidence URL and comparable versions are present.
page generated2026-08-03
manager version4.0.1
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:mummer |
|---|---|
| Version | 4.0.1 |
| Package manager | Homebrew |
| Homepage | https://github.com/mummer4/mummer |
| Repository | https://github.com/mummer4/mummer |
| Bottle | not recorded |
| Service | none declared |
source database matches
Other package-manager records
Matches are pulled from external package-manager indexes and kept separate from local Automic Vault package links.
Debian apt95%
mummer 3.23+dfsg-8
Efficient sequence alignment of full genomes
https://mummer.sourceforge.net/
sudo apt install mummer- Section: science
- Architecture: amd64
- 5 dependencies
- normalized package name match
- Matched by: Mummer
Debian apt95%
mummer-doc 3.23+dfsg-8
Documentation for MUMmer
https://mummer.sourceforge.net/
sudo apt install mummer-doc- Section: doc
- Architecture: all
- Source Package: mummer
- normalized package name match
- Matched by: Mummer
Ubuntu apt95%
mummer 3.23+dfsg-8
Efficient sequence alignment of full genomes
https://mummer.sourceforge.net/
sudo apt install mummer- Section: universe/science
- Architecture: amd64
- 5 dependencies
- normalized package name match
- Matched by: Mummer
Ubuntu apt95%
mummer-doc 3.23+dfsg-8
Documentation for MUMmer
https://mummer.sourceforge.net/
sudo apt install mummer-doc- Section: universe/doc
- Architecture: all
- Source Package: mummer
- normalized package name match
- Matched by: Mummer
source trail
Generated from repository data
This page is generated by av-web from the private package SQLite artifact built by scripts/generate-pkg-sqlite.py.
Combined YAML source
View the package source record on GitHub.
Used sources
- Geiger risk classifier
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- pkg.so package database
- pkgdb category and tag curation