# Install spoa with Homebrew, apt SIMD partial order alignment tool/library. Version 4.1.5 via Homebrew; verified 2026-06-21. ## Install ```sh sudo av install brew:spoa ``` Additional install commands: ### macOS - Homebrew (100%): ```sh brew install spoa ``` Evidence: local Homebrew formula metadata ### Linux - Debian apt (92%): ```sh sudo apt install libspoa-dev ``` Evidence: Debian stable package indexes: libspoa-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz ## Package facts - **Package key:** brew:spoa - **Package manager:** Homebrew - **Package manager page:** - **Version:** 4.1.5 - **Source summary:** SIMD partial order alignment tool/library - **Homepage:** - **Repository:** - **Upstream docs:** - **License:** MIT - **Source archive:** - **Last updated:** 2026-06-21T00:20:16Z - **Generated:** 2026-07-08T07:18:31+00:00 ## Executables - spoa (cli) - spoa (alias) ## Build dependencies - cmake ## Install behavior - Post-install hook: not defined - Bottle: available on arm64_linux, arm64_sequoia, arm64_sonoma, arm64_tahoe, sonoma, x86_64_linux ## Freshness - Page generated: 2026-07-08 - Package-manager version: 4.1.5 - Package-manager updated: 2026-06-21 - Local data: ok - Upstream repository: https://github.com/rvaser/spoa - Upstream latest detected: 4.1.5 (current) ## 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 - - source_facts.package-manager ## Security Notes library-like package without higher-risk signals. - **Geiger risk:** green / low - library-like package without higher-risk signals ## Source Database Details - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** spoa - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## Other Package-Manager Records - Debian apt - libspoa-dev - 4.1.4-2+b1: normalized package name match | Debian stable package indexes: libspoa-dev from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | SIMD partial order alignment library (development files) | https://github.com/rvaser/spoa - Debian apt - libspoa7.0.0 - 4.1.4-2+b1: normalized package name match | Debian stable package indexes: libspoa7.0.0 from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | SIMD partial order alignment library | https://github.com/rvaser/spoa - Debian apt - spoa - 4.1.4-2+b1: normalized package name match | Debian stable package indexes: spoa from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | SIMD partial order alignment tool | https://github.com/rvaser/spoa - Ubuntu apt - libspoa-dev - 4.0.8-1: normalized package name match | Ubuntu 24.04 LTS package indexes: libspoa-dev from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | SIMD partial order alignment library (development files) | https://github.com/rvaser/spoa - Ubuntu apt - libspoa7.0.0 - 4.0.8-1: normalized package name match | Ubuntu 24.04 LTS package indexes: libspoa7.0.0 from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | SIMD partial order alignment library | https://github.com/rvaser/spoa - Ubuntu apt - spoa - 4.0.8-1: normalized package name match | Ubuntu 24.04 LTS package indexes: spoa from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | SIMD partial order alignment tool | https://github.com/rvaser/spoa ## Related links - [Source-control packages](https://www.automicvault.com/pkg/source-control-tools/) - Belongs to a source-control command family. - [Terminal utility packages](https://www.automicvault.com/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Text processing packages](https://www.automicvault.com/pkg/text-processing-tools/) - Matched text, document, or structured-data processing metadata. - [Developer build packages](https://www.automicvault.com/pkg/developer-build-tools/) - Matched build, compiler, generator, or developer workflow metadata. - [cmake](https://www.automicvault.com/pkg/brew/cmake/) - Build dependency declared by Homebrew. - [cflow](https://www.automicvault.com/pkg/brew/cflow/) - Shares av.db curated category or tags: c, cli, developer-tools, static-analysis. - [cppcheck](https://www.automicvault.com/pkg/brew/cppcheck/) - Shares av.db curated category or tags: c, cli, developer-tools, static-analysis. - [datadog-static-analyzer](https://www.automicvault.com/pkg/brew/datadog-static-analyzer/) - Shares av.db curated category or tags: cli, developer-tools, security, static-analysis. - [kube-score](https://www.automicvault.com/pkg/brew/kube-score/) - Shares av.db curated category or tags: cli, developer-tools, security, static-analysis. - [scalastyle](https://www.automicvault.com/pkg/brew/scalastyle/) - Shares av.db curated category or tags: cli, developer-tools, lint, static-analysis. - [semgrep](https://www.automicvault.com/pkg/brew/semgrep/) - Shares av.db curated category or tags: cli, developer-tools, security, static-analysis. - [sparse](https://www.automicvault.com/pkg/brew/sparse/) - Shares av.db curated category or tags: c, cli, developer-tools, static-analysis. - [checkstyle](https://www.automicvault.com/pkg/brew/checkstyle/) - Shares av.db curated category or tags: cli, developer-tools, static-analysis. - [credo](https://www.automicvault.com/pkg/brew/credo/) - Local package facts share a topical domain. Shared terms: analysis, cli, developer, developer-tools, static. - [dscanner](https://www.automicvault.com/pkg/brew/dscanner/) - Local package facts share a topical domain. Shared terms: analysis, cli, developer, developer-tools, static. - [errcheck](https://www.automicvault.com/pkg/brew/errcheck/) - Local package facts share a topical domain. Shared terms: analysis, cli, developer, developer-tools, static. ## Combined YAML source View the package source record on GitHub. [combined/spoa.yml](https://github.com/automic-vault/db/blob/main/combined/spoa.yml) ## Sources - Nucleus package database - Geiger risk classifier - package-page enrichment - curated package history - package version freshness - av.db category and tag curation - package relationship graph - external package-manager database matches - cross-ecosystem install command graph