pkg.soopen package index

brew / rank 9283

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. Also installable with debian: sudo apt install abpoa.

Install commandSecurity notes

install

Additional install commands

macOS

Homebrewverified · 100%
brew install abpoa

local Homebrew formula metadata

Linux

Debian aptverified · 92%
sudo apt install abpoa

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

Nixverified · 92%
nix profile install nixpkgs#abpoa

nixpkgs 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

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.

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
abpoaexecutableindexed 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 version1.5.6
manager updated2026-05-26
local dataunknown
upstreamnot available
latest detectednot detected
  • okNo freshness warnings were generated.

install metadata

Package metadata

Package keybrew:abpoa
Version1.5.6
Package managerHomebrew
Homepagehttps://github.com/yangao07/abPOA
Repositoryhttps://github.com/yangao07/abPOA
Last updated2026-05-26T23:37:46-04:00
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%

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 stable package indexes · deb.debian.org · Debian stable package indexes: abpoa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
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
Debian stable package indexes · deb.debian.org · Debian stable package indexes: python3-pyabpoa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz
Nix95%

abpoa

nix profile install nixpkgs#abpoa
  • normalized package name match
  • Matched by: Abpoa
nixpkgs package indexes · api.github.com · nixpkgs package indexes: pkgs/by-name/ab/abpoa/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1
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 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: abpoa from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz
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
Ubuntu 24.04 LTS package indexes · archive.ubuntu.com · Ubuntu 24.04 LTS package indexes: python3-pyabpoa 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