使用 Homebrew, apt, dnf, MacPorts, Nix 安装 hmmer

项目链接

• 主页
• 仓库
• 上游文档
• 软件包管理器页面

命令和别名

• alimask
• hmmalign
• hmmbuild
• hmmconvert
• hmmemit
• hmmfetch
• hmmlogo
• hmmpgmd
• hmmpgmd_shard
• hmmpress
• hmmscan
• hmmsearch
• hmmsim
• hmmstat
• jackhmmer
• makehmmerdb
• nhmmer
• nhmmscan
• phmmer

项目历史

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.

采用历史

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.

使用方式

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.

为什么软件包爱好者会关心

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.

时间线

• 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.

来源

• https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/release-notes/HISTORY - official release lineage from HMMER1 through HMMER3.
• https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/release-notes/RELEASE-2.0 - official HMMER2 beta announcement and rewrite notes.
• https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/release-notes/RELEASE-3.0 - official HMMER3 production release notes and early adoption notes.
• https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/release-notes/RELEASE-3.3.md - official HMMER 3.3 notes for hmmpgmd sharding and deep-alignment changes.
• https://raw.githubusercontent.com/EddyRivasLab/hmmer/master/release-notes/RELEASE-3.4.md - official HMMER 3.4 notes for Apple Silicon and sanitizer work.