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brew / rank 6610

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. Also installable with debian: sudo apt install kalign.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install kalign

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install kalign

Debian stable package indexes · kalign · source: deb.debian.org

Nixverified · 92%
nix profile install nixpkgs#kalign

nixpkgs package indexes · pkgs/by-name/ka/kalign/package.nix · source: api.github.com

overview

Package summary

Fast multiple sequence alignment program for biological sequences

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.

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

CommandKindExposureNote
kalignexecutableindexed executableDiscovered 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 version3.5.1
manager updated
local dataunknown
upstreamnot available
latest detectednot detected
  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:kalign
Version3.5.1
Package managerHomebrew
Homepagehttps://github.com/TimoLassmann/kalign
Repositoryhttps://github.com/TimoLassmann/kalign
Bottlenot recorded
Servicenone 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%

kalign 1:3.4.0-1+b3

Global and progressive multiple sequence alignment

https://msa.sbc.su.se/

sudo apt install kalign
  • Section: science
  • Architecture: amd64
  • Source Package: kalign
  • 2 dependencies
  • normalized package name match
  • Matched by: Kalign
Debian stable package indexes · deb.debian.org · Debian stable package indexes: kalign from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

kalign

nix profile install nixpkgs#kalign
  • normalized package name match
  • Matched by: Kalign
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ka/kalign/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
Ubuntu apt95%

kalign 1:3.3.5-1

Global and progressive multiple sequence alignment

https://msa.sbc.su.se/

sudo apt install kalign
  • Section: universe/science
  • Architecture: amd64
  • 2 dependencies
  • normalized package name match
  • Matched by: Kalign
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: kalign from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz

package graph

Links come from deterministic package relationships, av.db category and tag curation, ecosystem matches, and package hub membership.

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.

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