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Install spoa with Homebrew, apt

SIMD partial order alignment tool/library. Version 4.1.5 via Homebrew; verified 2026-06-21. Also installable with debian: sudo apt install libspoa-dev.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install spoa

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install spoa

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

overview

Package summary

SIMD partial order alignment tool/library

Commands and aliases

  • spoa

history

Project history and usage

Spoa is a C++ SIMD implementation of partial order alignment, packaged as both a command-line tool and library for generating consensus sequences from biological sequence reads.

Project history

The official README defines Spoa as `SIMD POA`, an implementation of the partial order alignment algorithm used to generate consensus sequences. It supports local, global, and semi-global alignment modes, linear, affine, and convex gap modes, and SIMD acceleration through SSE4.1+, AVX2, SIMDe, and dispatching.

Spoa is tied to the long-read sequencing era: the README points to the original POA and consensus-sequence literature, while the project is also marked as published in Genome Research. In package form, it gives bioinformatics pipelines a small native executable and a linkable library rather than a large workflow framework.

Adoption history

The supplied package-manager data lists Spoa in Homebrew and as `libspoa-dev` in Debian and Ubuntu. That packaging split reflects its dual role: command for direct FASTA/FASTQ processing and development library for other genomics tools.

How it is used

The `spoa` command reads FASTA or FASTQ sequences, including gzip-compressed input, and writes consensus or multiple-sequence-alignment FASTA output. Options select scoring, gap penalties, alignment mode, and result mode.

Why package nerds care

Spoa matters to package maintainers because it is a compact, performance-sensitive C++ bioinformatics dependency. Its optional SIMD/SIMDe paths and library install targets are exactly the kind of details that determine whether a formula or distro package is useful beyond a single architecture.

Timeline

  • 2002: Partial order alignment is published in Bioinformatics, the algorithmic foundation cited by the Spoa README.
  • 2003: Consensus sequence generation with partial order graphs is published, also cited by the Spoa README.
  • 2017: Spoa is associated with a Genome Research publication badge in the official repository.
  • Ongoing: The README documents CMake and Meson builds plus SIMD and portability options.

Related projects

  • The original POA algorithm and consensus-sequence papers are cited by the official Spoa README.
  • SIMDe is listed as a portability option for SIMD support.
  • bioparser and biosoup are listed as dependencies for the executable and tests.

security posture

Risk level: green

library-like package without higher-risk signals.

Risk classifier

green risk · low confidence · appliance

Why

  • library-like package without higher-risk signals

Signals

  • metadata:library-like

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
spoaexecutableindexed 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 version4.1.5
manager updated2026-06-21
local dataunknown
upstreamnot available
latest detectednot detected
  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:spoa
Version4.1.5
Package managerHomebrew
Homepagehttps://github.com/rvaser/spoa
Repositoryhttps://github.com/rvaser/spoa
Last updated2026-06-21T00:20:16Z
Pulseupdated
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%

libspoa-dev 4.1.4-2+b1

SIMD partial order alignment library (development files)

https://github.com/rvaser/spoa

sudo apt install libspoa-dev
  • Section: libdevel
  • Architecture: amd64
  • Source Package: spoa
  • 2 dependencies
  • normalized package name match
  • Matched by: Spoa
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libspoa-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

libspoa7.0.0 4.1.4-2+b1

SIMD partial order alignment library

https://github.com/rvaser/spoa

sudo apt install libspoa7.0.0
  • Section: libs
  • Architecture: amd64
  • Source Package: spoa
  • 3 dependencies
  • normalized package name match
  • Matched by: Spoa
Debian stable package indexes · deb.debian.org · Debian stable package indexes: libspoa7.0.0 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Debian apt95%

spoa 4.1.4-2+b1

SIMD partial order alignment tool

https://github.com/rvaser/spoa

sudo apt install spoa
  • Section: science
  • Architecture: amd64
  • Source Package: spoa
  • 5 dependencies
  • normalized package name match
  • Matched by: Spoa
Debian stable package indexes · deb.debian.org · Debian stable package indexes: spoa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Ubuntu apt95%

libspoa-dev 4.0.8-1

SIMD partial order alignment library (development files)

https://github.com/rvaser/spoa

sudo apt install libspoa-dev
  • Section: universe/libdevel
  • Architecture: amd64
  • Source Package: spoa
  • 2 dependencies
  • normalized package name match
  • Matched by: Spoa
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libspoa-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

libspoa7.0.0 4.0.8-1

SIMD partial order alignment library

https://github.com/rvaser/spoa

sudo apt install libspoa7.0.0
  • Section: universe/libs
  • Architecture: amd64
  • Source Package: spoa
  • 3 dependencies
  • normalized package name match
  • Matched by: Spoa
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: libspoa7.0.0 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
Ubuntu apt95%

spoa 4.0.8-1

SIMD partial order alignment tool

https://github.com/rvaser/spoa

sudo apt install spoa
  • Section: universe/science
  • Architecture: amd64
  • 5 dependencies
  • normalized package name match
  • Matched by: Spoa
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: spoa 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