# hmmer を Homebrew, apt, dnf, MacPorts, Nix でインストール hmmer のインストール経路、実行ファイル、メタデータ、AI エージェント向けセキュリティノートを確認します。 ## インストール ```sh sudo av install brew:hmmer ``` 追加のインストールコマンド: ### macOS - Homebrew (100%): ```sh brew install hmmer ``` 証拠: local Homebrew formula metadata - MacPorts (94%): ```sh sudo port install hmmer ``` 証拠: MacPorts ports tree: science/hmmer/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ### Linux - Debian apt (92%): ```sh sudo apt install hmmer ``` 証拠: Debian stable package indexes: hmmer from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz - dnf (92%): ```sh sudo dnf install hmmer ``` 証拠: Fedora Rawhide package metadata: hmmer from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst - Nix (92%): ```sh nix profile install nixpkgs#hmmer ``` 証拠: nixpkgs package indexes: pkgs/by-name/hm/hmmer/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 ## パッケージ情報 - **パッケージキー:** brew:hmmer - **パッケージマネージャ:** Homebrew - **パッケージマネージャページ:** - **バージョン:** 3.4 - **ソース概要:** Build profile HMMs and scan against sequence databases - **ホームページ:** - **リポジトリ:** - **上流ドキュメント:** - **ライセンス:** BSD-3-Clause - **ソースアーカイブ:** - **生成日時:** 2026-07-08T18:08:21+00:00 ## 実行可能ファイル - alimask (cli) - hmmalign (cli) - hmmbuild (cli) - hmmconvert (cli) - hmmemit (cli) - hmmfetch (cli) - hmmlogo (cli) - hmmpgmd (cli) - hmmpgmd_shard (cli) - hmmpress (cli) - hmmscan (cli) - hmmsearch (cli) - hmmsim (cli) - hmmstat (cli) - jackhmmer (cli) - makehmmerdb (cli) - nhmmer (cli) - nhmmscan (cli) - phmmer (cli) - alimask (エイリアス) - hmmalign (エイリアス) - hmmbuild (エイリアス) - hmmconvert (エイリアス) - hmmemit (エイリアス) - hmmfetch (エイリアス) - hmmlogo (エイリアス) - hmmpgmd (エイリアス) - hmmpgmd_shard (エイリアス) - hmmpress (エイリアス) - hmmscan (エイリアス) - hmmsearch (エイリアス) - hmmsim (エイリアス) - hmmstat (エイリアス) - jackhmmer (エイリアス) - makehmmerdb (エイリアス) - nhmmer (エイリアス) - nhmmscan (エイリアス) - phmmer (エイリアス) ## インストール挙動 - post-install フック: 未定義 - Bottle: 利用可能 対象 arm64_big_sur, arm64_linux, arm64_monterey, arm64_sequoia, arm64_sonoma, arm64_tahoe, arm64_ventura, big_sur, monterey, sonoma, ventura, x86_64_linux ## バージョンと鮮度 - ページ生成日: 2026-07-08 - マネージャ版: 3.4 - ローカルデータ: OK - 上流リポジトリ: http://hmmer.org/ - 情報: No package-manager update timestamp was available. - 情報: Release/tag comparison is only available for GitHub repositories. ## プロジェクトの歴史と使われ方 HMMER is a long-running bioinformatics toolkit for sequence homology search, multiple-sequence-alignment work, and profile hidden Markov model workflows. Its package identity is unusually strong because installing it gives a family of command-line programs, including hmmbuild, hmmsearch, hmmscan, phmmer, jackhmmer, nhmmer, and hmmpress, rather than a single executable. ### プロジェクトの歴史 The official release history traces HMMER1 to Sean Eddy's work at MRC-LMB Cambridge and Washington University, with a local release in April 1994 and the first public release in July 1994. HMMER2 followed at Washington University, with the 2.0 beta described as a nearly complete rewrite for profile hidden Markov model analysis of protein sequences and the 2.1 series becoming the first public 2.x release in October 1998. HMMER3 development moved through HHMI Janelia Farm and Harvard University. The 3.0 release notes describe 3.0 as production-ready after beta testing that began in January 2009, and note that beta versions were already deployed for Pfam, InterPro, and other protein databases before the stable 3.0 release. Later HMMER3 work added DNA-oriented tools, web-server support paths, MPI and daemon improvements, performance fixes, and platform support. ### 採用の歴史 The official README says HMMER is used by many protein-family domain databases and large-scale annotation pipelines, including many members of the InterPro Consortium. That sentence captures why it became a standard Unix bioinformatics package: it sits behind databases and annotation systems that many users consume indirectly, while still remaining a scriptable command-line toolkit for local analysis. HMMER also spread through packaging because it is portable C software with a conventional configure, make, make check, and make install workflow. The Homebrew formula and the supplied package facts show it appearing under the same package name across common Unix-like package managers, which makes recipes, tutorials, and analysis pipelines relatively stable across macOS, Linux distributions, and reproducible-environment tools. ### 使われ方 Typical HMMER usage starts with building or obtaining a profile HMM, preparing a sequence or HMM database, and running search tools such as hmmsearch, hmmscan, phmmer, jackhmmer, nhmmer, or nhmmscan. The README points users to the User's Guide tutorial after installation, while release notes show continuing attention to search daemons, sharded databases, multithreading behavior, FM-index handling, and profile-building behavior on deep alignments. For package users, HMMER is often consumed as a command-line dependency inside larger biological-data workflows. The tools are small enough to script directly, but important enough that subtle version changes, database-pressing formats, CPU behavior, and bundled Easel-library changes can matter to reproducible science pipelines. ### パッケージ好きにとっての重要性 HMMER is package-nerd significant because it is a classic scientific CLI package with real downstream consequences. It has many executables, a long release lineage, a bundled support library, man pages and PDFs, and a user base that cares about exact scoring behavior and reproducibility. It is also a good example of bioinformatics packaging culture: upstream tarballs are still recommended for release builds, GitHub is used for development, package managers provide convenience installs, and downstream users expect the same tool names to work inside shell scripts, HPC jobs, Docker images, notebooks, and workflow managers. ### タイムライン - 1994: HMMER1 first public release. - 1998: HMMER2 beta announced as a near-complete rewrite for profile HMM analysis. - 1998: HMMER 2.1 became the first public release of the 2.x series. - 2010: HMMER 3.0 released after beta deployments in Pfam, InterPro, and other protein databases. - 2019: HMMER 3.3 improved hmmpgmd sharding and profile-building behavior on deep alignments. - 2023: HMMER 3.4 added Apple Silicon ARM support and sanitizer-driven fixes. ### Related projects - Easel is the closest companion codebase because the HMMER README says HMMER development depends on the Eddy/Rivas lab's Easel library. Infernal is related through the repository workflow note that the HMMER3 stable branch is used when H3 is released as a library inside Infernal. - Pfam and InterPro are the major adoption-related projects named by upstream sources. They explain why HMMER matters beyond direct command-line users: protein-family databases and annotation pipelines amplify HMMER's model formats, search behavior, and package availability. ### ソース - - - - - ## セキュリティノート broad file, network, media, or database tool signal. - **Geiger リスク:** blue / 中 - broad file, network, media, or database tool signal ## ソースデータベース詳細 - **Source Database:** Homebrew formula API - **Tap:** homebrew/core - **Full Name:** hmmer - **Version Scheme:** 0 - **Revision:** 0 - **Bottle Stable Root URL:** - **Deprecated:** no - **Disabled:** no - **Keg Only:** no - **URL Keys:** stable ## 他のパッケージマネージャ記録 - Debian apt - hmmer - 3.4+dfsg-2: normalized package name match | Debian stable package indexes: hmmer from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | profile hidden Markov models for protein sequence analysis | http://hmmer.org/ - Debian apt - hmmer-doc - 3.4+dfsg-2: normalized package name match | Debian stable package indexes: hmmer-doc from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | profile hidden Markov models for protein sequence analysis (docs) | http://hmmer.org/ - Debian apt - hmmer-examples - 3.4+dfsg-2: normalized package name match | Debian stable package indexes: hmmer-examples from https://deb.debian.org/debian/dists/stable/main/binary-amd64/Packages.xz | profile hidden Markov models for protein sequence analysis (examples) | http://hmmer.org/ - Nix - hmmer: normalized package name match | nixpkgs package indexes: pkgs/by-name/hm/hmmer/package.nix from https://api.github.com/repos/NixOS/nixpkgs/git/trees/master?recursive=1 - Ubuntu apt - hmmer - 3.4+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: hmmer from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | profile hidden Markov models for protein sequence analysis | http://hmmer.org/ - Ubuntu apt - hmmer-doc - 3.4+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: hmmer-doc from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | profile hidden Markov models for protein sequence analysis (docs) | http://hmmer.org/ - Ubuntu apt - hmmer-examples - 3.4+dfsg-2: normalized package name match | Ubuntu 24.04 LTS package indexes: hmmer-examples from https://archive.ubuntu.com/ubuntu/dists/noble/universe/binary-amd64/Packages.gz | profile hidden Markov models for protein sequence analysis (examples) | http://hmmer.org/ - dnf - hmmer - 3.3.2-12.fc44: normalized package name match | Fedora Rawhide package metadata: hmmer from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | Biosequence analysis using profile hidden Markov models | http://hmmer.org - dnf - hmmer-doc - 3.3.2-12.fc44: normalized package name match | Fedora Rawhide package metadata: hmmer-doc from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | Documentation for hmmer | http://hmmer.org - dnf - hmmer-easel - 3.3.2-12.fc44: normalized package name match | Fedora Rawhide package metadata: hmmer-easel from https://dl.fedoraproject.org/pub/fedora/linux/development/rawhide/Everything/x86_64/os/repodata/e5ca8ce900cd68f5419e1c39ae517343100b306336cbaeb70a3c153121d95094-primary.xml.zst | Easel collection of small tools | http://hmmer.org - MacPorts - hmmer: normalized package name match | MacPorts ports tree: science/hmmer/Portfile from https://api.github.com/repos/macports/macports-ports/git/trees/master?recursive=1 ## 関連リンク - [Secret-risk packages](https://www.automicvault.com/ja/pkg/secret-risk-packages/) - Has protected-tool coverage, approval-gate, or non-low Geiger security signals. - [Terminal utility packages](https://www.automicvault.com/ja/pkg/terminal-utilities/) - Matched terminal and command-line workflow metadata. - [Text processing packages](https://www.automicvault.com/ja/pkg/text-processing-tools/) - Matched text, document, or structured-data processing metadata. - [Developer build packages](https://www.automicvault.com/ja/pkg/developer-build-tools/) - Matched build, compiler, generator, or developer workflow metadata. - [mmseqs2](https://www.automicvault.com/ja/pkg/brew/mmseqs2/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis, sequence-search. - [seqkit](https://www.automicvault.com/ja/pkg/brew/seqkit/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis. - [seqtk](https://www.automicvault.com/ja/pkg/brew/seqtk/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-analysis. - [abpoa](https://www.automicvault.com/ja/pkg/brew/abpoa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [blast](https://www.automicvault.com/ja/pkg/brew/blast/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [bwa](https://www.automicvault.com/ja/pkg/brew/bwa/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [diamond](https://www.automicvault.com/ja/pkg/brew/diamond/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. - [lastz](https://www.automicvault.com/ja/pkg/brew/lastz/) - Shares av.db curated category or tags: bioinformatics, cli, science, sequence-alignment. ## Combined YAML source View the package source record on GitHub. [combined/hmmer.yml](https://github.com/automic-vault/db/blob/main/combined/hmmer.yml) ## ソース - 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