macOS
Homebrewverified · 100%
brew install abpoalocal Homebrew formula metadata
brew
Install abpoa with Homebrew, apt, Nix
SIMD-based C library for fast partial order alignment using adaptive band. Version 1.5.6 via Homebrew; verified 2026-05-26.
install
Additional install commands
Linux
Debian aptverified · 92%
sudo apt install abpoaDebian stable package indexes · abpoa · source: deb.debian.org
Nixverified · 92%
nix profile install nixpkgs#abpoanixpkgs package indexes · pkgs/by-name/ab/abpoa/package.nix · source: api.github.com
overview
Package summary
SIMD-based C library for fast partial order alignment using adaptive band
Project links
Commands and aliases
- abpoa
history
Project history and usage
abPOA is a C library and command-line tool for adaptive-banded partial-order alignment, multiple sequence alignment, and consensus generation. Package maintainers care about it because it exposes a performance-sensitive bioinformatics primitive as a small buildable C package with command-line, conda, Homebrew, and Python-facing usage.
Project history
The first GitHub release, v1.0.0, was published on April 15, 2020. The project was described in Bioinformatics later in 2020 as an SIMD-based C library for fast partial order alignment using adaptive banding, and the upstream README presents it as an extended version of partial-order alignment with adaptive banded dynamic programming and SIMD implementation.
Adoption history
The README documents installation via conda and Homebrew, source builds, prebuilt Linux and macOS binaries, and a pyabpoa Python package. The input metadata also shows distribution packaging in Homebrew, Debian, Nix, and Ubuntu, which is typical for bioinformatics tools that need both reproducible workflows and local command-line execution.
How it is used
abPOA accepts FASTA, FASTQ, and gzip-compressed FASTA/FASTQ input, performs sequence-to-graph alignment, emits consensus FASTA by default, and can also emit row-column MSA, GFA graph output, amino-acid consensus, and graph plots. The README documents global, local, and extension alignment modes plus linear, affine, and convex gap penalties.
Why package nerds care
The package is significant because it turns a common long-read consensus and MSA building block into a portable SIMD-aware command-line dependency. Its release notes continue to mention packaging-facing work such as pyproject.toml for pyabpoa and SIMD dispatch.
Timeline
- 2020: First public GitHub release v1.0.0.
- 2020: Bioinformatics article published for abPOA.
- 2025: v1.5.4 added SIMD dispatch and Python 3.13 installation fixes.
- 2026: v1.5.6 added easier incremental MSA and pyproject.toml for pyabpoa.
Related projects
- The README explicitly frames abPOA as an extension of partial-order alignment and references heaviest bundling for consensus generation. It also ships pyabpoa for Python users and connects to Bioconda and Homebrew packaging for workflow installation.
Sources
- https://doi.org/10.1093/bioinformatics/btaa963
- https://github.com/yangao07/abPOA#readme
- https://github.com/yangao07/abPOA/releases
- input 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.
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 |
|---|---|---|---|
abpoa | 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 version1.5.6
manager updated2026-05-26
local dataok
upstreamnot checked
latest detectednot detected
https://github.com/yangao07/abPOA
- infoNo cached GitHub release or tag data was available.https://github.com/yangao07/abPOAnone confidence
install metadata
Package metadata
| Package key | brew:abpoa |
|---|---|
| Version | 1.5.6 |
| Package manager | Homebrew |
| Package manager page | https://formulae.brew.sh/formula/abpoa |
| Homepage | https://github.com/yangao07/abPOA |
| Repository | https://github.com/yangao07/abPOA |
| Upstream docs | https://doi.org/10.1093/bioinformatics/btaa963 |
| License | MIT |
| Source archive | https://github.com/yangao07/abPOA/releases/download/v1.5.6/abPOA-v1.5.6.tar.gz |
| Last updated | 2026-05-26T23:37:46-04:00 |
| Pulse | updated |
| 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 | abpoa |
| Version Scheme | 0 |
| Revision | 0 |
| Head Version | HEAD |
| 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%
abpoa 1.5.3-1+b4
adaptive banded Partial Order Alignment
https://github.com/yangao07/abPOA
sudo apt install abpoa- Section: science
- Architecture: amd64
- Source Package: abpoa
- 3 dependencies
- normalized package name match
- Matched by: Abpoa
Debian apt95%
python3-pyabpoa 1.5.3-1+b4
adaptive banded Partial Order Alignment - python3 module
https://github.com/yangao07/abPOA
sudo apt install python3-pyabpoa- Section: python
- Architecture: amd64
- Source Package: abpoa
- 3 dependencies
- normalized package name match
- Matched by: Abpoa
Nix95%
abpoa
nix profile install nixpkgs#abpoa- normalized package name match
- Matched by: Abpoa
Ubuntu apt95%
abpoa 1.5.1-1build1
adaptive banded Partial Order Alignment
https://github.com/yangao07/abPOA
sudo apt install abpoa- Section: universe/science
- Architecture: amd64
- 3 dependencies
- normalized package name match
- Matched by: Abpoa
Ubuntu apt95%
python3-pyabpoa 1.5.1-1build1
adaptive banded Partial Order Alignment - python3 module
https://github.com/yangao07/abPOA
sudo apt install python3-pyabpoa- Section: universe/python
- Architecture: amd64
- Source Package: abpoa
- 3 dependencies
- normalized package name match
- Matched by: Abpoa
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