macOS
Homebrewverified · 100%
brew install kalignlocal Homebrew formula metadata
brew
Install kalign with Homebrew, apt, Nix
Fast multiple sequence alignment program for biological sequences. Version 3.5.1 via Homebrew; verified from local package data.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install kalignDebian stable package indexes · kalign · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#kalignnixpkgs package indexes · pkgs/by-name/ka/kalign/package.nix · source: api.github.com
overview
Package summary
Fast multiple sequence alignment program for biological sequences
Project links
Commands and aliases
- kalign
history
Project history and usage
Kalign is a fast multiple-sequence-alignment program for protein, DNA, and RNA sequences, distributed as a command-line bioinformatics tool.
Project history
Timo Lassmann and Erik Sonnhammer published the original Kalign method in BMC Bioinformatics on 2005-12-12. The paper described a Wu-Manber-based progressive alignment method intended to improve both speed and accuracy for large comparative-genomics workloads.
Adoption history
Kalign remained in the bioinformatics toolchain because multiple sequence alignment is a routine upstream step for homology, conserved-motif, phylogeny, and structure-oriented analyses. Kalign 3, published in Bioinformatics in 2019, was presented as a complete rewrite to handle larger protein and nucleotide sequence sets, using SIMD-accelerated distance estimation and fast guide-tree construction.
How it is used
Users run kalign on FASTA-like biological sequence inputs to produce multiple alignments. The modern README describes progressive alignment with multi-threading support, source builds with CMake, and alternatives such as Zig builds and Python packaging.
Why package nerds care
Kalign is a classic science CLI package: a published algorithm wrapped in a small executable, useful in scripts and pipelines, with package-manager availability making a cited method reproducible without hand-building a lab-specific binary.
Timeline
- 2005-12-12: Original Kalign paper published in BMC Bioinformatics.
- 2019-10-26: Kalign 3 paper published in Bioinformatics.
- 2019-10-28: GitHub release 3.1 published.
- 2020-11-06: v3.3 release added multi-threading.
- 2026-02-27: Kalign 3.5.1 published.
Related projects
- Related multiple-sequence-alignment tools include ClustalW, MAFFT, MUSCLE, T-Coffee, and other progressive or consistency-based MSA programs.
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 post-install hook is recorded in formula metadata.
- Homebrew bottle metadata is available for 6 platform targets.
- Installs with 1 runtime dependencies.
- Build metadata lists 1 build dependencies.
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 |
|---|---|---|---|
kalign | cli | global executable |
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 generated2026-07-08
manager version3.5.1
manager updated
local dataok
upstreamcurrent
latest detectedv3.5.1
https://github.com/TimoLassmann/kalign
- infoNo package-manager update timestamp was available.low confidence
install metadata
Package metadata
| Package key | brew:kalign |
|---|---|
| Version | 3.5.1 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/kalign |
| Homepage | https://github.com/TimoLassmann/kalign |
| Repository | https://github.com/TimoLassmann/kalign |
| Upstream docs | https://github.com/TimoLassmann/kalign#readme |
| License | Apache-2.0 |
| Source archive | https://github.com/TimoLassmann/kalign/archive/refs/tags/v3.5.1.tar.gz |
| Dependencies | libomp |
| Build dependencies | cmake |
| Bottle | available (on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | not defined |
| Service | none declared |
registry facts
Source database details
| Source Database | Homebrew formula API |
|---|---|
| Tap | homebrew/core |
| Full Name | kalign |
| Version Scheme | 0 |
| Revision | 0 |
| Bottle Stable Root URL | https://ghcr.io/v2/homebrew/core |
| Deprecated | no |
| Disabled | no |
| Keg Only | no |
| URL Keys |
|
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%
kalign 1:3.4.0-1+b3
Global and progressive multiple sequence alignment
sudo apt install kalign- Section: science
- Architecture: amd64
- Source Package: kalign
- 2 dependencies
- normalized package name match
- Matched by: Kalign
Nix95%
kalign
nix profile install nixpkgs#kalign- normalized package name match
- Matched by: Kalign
Ubuntu apt95%
kalign 1:3.3.5-1
Global and progressive multiple sequence alignment
sudo apt install kalign- Section: universe/science
- Architecture: amd64
- 2 dependencies
- normalized package name match
- Matched by: Kalign
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
- Nucleus package database
- av.db category and tag curation
- cross-ecosystem install command graph
- curated package history
- external package-manager database matches
- package relationship graph
- package version freshness
- package-page enrichment