macOS
Homebrewverified · 100%
brew install spoalocal Homebrew formula metadata
brew
Install spoa with Homebrew, apt
SIMD partial order alignment tool/library. Version 4.1.5 via Homebrew; verified 2026-06-21.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install libspoa-devDebian stable package indexes · libspoa-dev · source: deb.debian.org
overview
Package summary
SIMD partial order alignment tool/library
Project links
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.
Sources
- https://github.com/rvaser/spoa#readme
- source_facts.package-manager
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 post-install hook is recorded in formula metadata.
- Homebrew bottle metadata is available for 6 platform targets.
- 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 |
|---|---|---|---|
spoa | 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 version4.1.5
manager updated2026-06-21
local dataok
upstreamcurrent
latest detected4.1.5
https://github.com/rvaser/spoa
- okNo freshness warnings were generated.
install metadata
Package metadata
| Package key | brew:spoa |
|---|---|
| Version | 4.1.5 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/spoa |
| Homepage | https://github.com/rvaser/spoa |
| Repository | https://github.com/rvaser/spoa |
| Upstream docs | https://github.com/rvaser/spoa#readme |
| License | MIT |
| Source archive | https://github.com/rvaser/spoa/archive/refs/tags/4.1.5.tar.gz |
| Last updated | 2026-06-21T00:20:16Z |
| Pulse | updated |
| 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 | spoa |
| 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%
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 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 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
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 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 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
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