macOS
Homebrew已验证 · 100%
brew install abpoalocal Homebrew formula metadata
安装
其他安装命令
Linux
Nix已验证 · 92%
nix profile install nixpkgs#abpoanixpkgs package indexes · pkgs/by-name/ab/abpoa/package.nix · 来源: api.github.com
概览
软件包摘要
SIMD-based C library for fast partial order alignment using adaptive band
历史
项目历史与用法
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.
项目历史
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.
采用历史
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.
使用方式
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.
为什么软件包爱好者会关心
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.
时间线
- 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.
来源
- https://doi.org/10.1093/bioinformatics/btaa963
- https://github.com/yangao07/abPOA#readme
- https://github.com/yangao07/abPOA/releases
- input source_facts.package-manager
安全态势
风险级别：绿色
library-like package without higher-risk signals.
风险分类器
绿色 风险 · 低 置信度 · appliance
原因
- library-like package without higher-risk signals
信号
- metadata:library-like
安装行为
- formula 元数据中未记录 Homebrew post-install 钩子。
- Homebrew bottle 元数据适用于 6 个平台目标。
建议审查
在无人值守的代理使用前，请检查该工具是否读取明文凭据、写入远程状态、发布制品或调用插件。
可执行文件
已安装的可执行文件
| 命令 | 类型 | 暴露范围 | 备注 |
|---|---|---|---|
abpoa | cli | 全局可执行文件 |
新鲜度
版本和新鲜度
这些信号区分页生成时间、软件包管理器活动和上游发布比较。只有存在证据 URL 和可比较版本时，才会提示版本落后。
页面生成时间2026-07-08
管理器版本1.5.6
管理器更新时间2026-05-26
本地数据OK
上游not checked
检测到的最新版本未检测到
https://github.com/yangao07/abPOA
- 信息No cached GitHub release or tag data was available.https://github.com/yangao07/abPOAnone 置信度
安装元数据
软件包元数据
| 软件包键 | brew:abpoa |
|---|---|
| 版本 | 1.5.6 |
| 软件包管理器 | Homebrew |
| 软件包管理器页面 | https://formulae.brew.sh/formula/abpoa |
| 主页 | https://github.com/yangao07/abPOA |
| 仓库 | https://github.com/yangao07/abPOA |
| 上游文档 | https://doi.org/10.1093/bioinformatics/btaa963 |
| 许可证 | MIT |
| 源码归档 | https://github.com/yangao07/abPOA/releases/download/v1.5.6/abPOA-v1.5.6.tar.gz |
| 最后更新 | 2026-05-26T23:37:46-04:00 |
| Pulse | updated |
| Bottle | 可用 (于 arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux) |
| Homebrew post-install | 未定义 |
| 服务 | 未声明 |
注册表事实
源数据库详情
| 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 |
|
源数据库匹配
其他软件包管理器记录
匹配项来自外部软件包管理器索引，并与本地 Automic Vault 软件包链接分开显示。
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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：Abpoa
Nix95%
abpoa
nix profile install nixpkgs#abpoa- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：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 依赖
- normalized package name match
- 匹配方式：Abpoa
来源线索
由仓库数据生成
此页面由 av-web 从 scripts/generate-pkg-sqlite.py 生成的私有软件包 SQLite 工件提供。
Combined YAML source
View the package source record on GitHub.
使用的来源
- 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