{"id":13751666,"url":"https://github.com/soedinglab/hh-suite","last_synced_at":"2025-04-14T05:19:22.610Z","repository":{"id":31468304,"uuid":"35032303","full_name":"soedinglab/hh-suite","owner":"soedinglab","description":"Remote protein homology detection suite.","archived":false,"fork":false,"pushed_at":"2024-11-08T02:28:11.000Z","size":24033,"stargazers_count":568,"open_issues_count":170,"forks_count":139,"subscribers_count":24,"default_branch":"master","last_synced_at":"2025-04-14T05:19:13.248Z","etag":null,"topics":["alignment","bioinformatics","cpp","hh-suite","hhblits","hhpred","hhsearch","opensource","profile-profile-search","profile-search","protein-structure","sequence-search","simd","viterbi"],"latest_commit_sha":null,"homepage":"https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3019-7","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/soedinglab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-05-04T12:00:48.000Z","updated_at":"2025-04-06T22:35:41.000Z","dependencies_parsed_at":"2022-08-08T10:16:01.377Z","dependency_job_id":"b0c9d8de-6942-40c8-b4b4-3f8bb2d1bdf7","html_url":"https://github.com/soedinglab/hh-suite","commit_stats":{"total_commits":1208,"total_committers":69,"mean_commits":"17.507246376811594","dds":0.8286423841059603,"last_synced_commit":"4c0cd66434ce0b83ccd247053f57989fdd53d82b"},"previous_names":[],"tags_count":8,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fhh-suite","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fhh-suite/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fhh-suite/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/soedinglab%2Fhh-suite/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/soedinglab","download_url":"https://codeload.github.com/soedinglab/hh-suite/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248824733,"owners_count":21167350,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["alignment","bioinformatics","cpp","hh-suite","hhblits","hhpred","hhsearch","opensource","profile-profile-search","profile-search","protein-structure","sequence-search","simd","viterbi"],"created_at":"2024-08-03T09:00:51.450Z","updated_at":"2025-04-14T05:19:22.586Z","avatar_url":"https://github.com/soedinglab.png","language":"C","readme":"# HH-suite3 for sensitive sequence searching\n\n(C) Johannes Soeding, Markus Meier, Martin Steinegger, Milot Mirdita, Michael Remmert, Andreas Hauser, Andreas Biegert\n\n[![BioConda Install](https://img.shields.io/conda/dn/bioconda/hhsuite.svg?style=flag\u0026label=BioConda%20install)](https://anaconda.org/bioconda/hhsuite)\n[![Biocontainer Pulls](https://img.shields.io/endpoint?url=https%3A%2F%2Fmmseqs.com%2Fbiocontainer.php%3Fcontainer%3Dhhsuite)](https://biocontainers.pro/#/tools/hhsuite)\n[![Github All Releases](https://img.shields.io/github/downloads/soedinglab/hh-suite/total.svg)](https://github.com/soedinglab/hh-suite/releases/latest)\n[![Docker Pulls](https://img.shields.io/docker/pulls/soedinglab/hh-suite.svg)](https://hub.docker.com/r/soedinglab/hh-suite)\n[![Build Status](https://dev.azure.com/themartinsteinegger/hhsuite/_apis/build/status/soedinglab.hh-suite?branchName=master)](https://dev.azure.com/themartinsteinegger/hhsuite/_build/latest?definitionId=4\u0026branchName=master)\n\nThe HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).\n\n## Documentation\n\nWe provide an extensive [user guide](https://github.com/soedinglab/hh-suite/wiki) with many usage examples, frequently asked questions and guides to build your own databases. \n\n### Installation\n\nHH-suite3 can also be installed by downloading a statically compiled version, [conda](https://github.com/conda/conda) or [Docker](https://github.com/moby/moby). HH-suite3 requires a 64-bit system (check with `uname -a | grep x86_64`). On AMD/Intel CPUs it requires at least support for the SSE2 instruction set (check by executing `cat /proc/cpuinfo | grep sse2` on Linux or `sysctl -a | grep machdep.cpu.features | grep SSE2` on macOS). `AVX2` is roughly 2x faster compared to SSE2. HH-suite3 also works on Linux systems with ARM64 and PPC64LE CPUs. Precompiled binaries for all supported systems can be found at [mmseqs.com/hhsuite](https://mmseqs.com/hhsuite).\n\n```\n# install via conda\nconda install -c conda-forge -c bioconda hhsuite \n# install docker\ndocker pull soedinglab/hh-suite\n# static SSE2 build\nwget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-SSE2-Linux.tar.gz; tar xvfz hhsuite-3.3.0-SSE2-Linux.tar.gz; export PATH=\"$(pwd)/bin:$(pwd)/scripts:$PATH\"\n# static AVX2 build\nwget https://github.com/soedinglab/hh-suite/releases/download/v3.3.0/hhsuite-3.3.0-AVX2-Linux.tar.gz; tar xvfz hhsuite-3.3.0-AVX2-Linux.tar.gz; export PATH=\"$(pwd)/bin:$(pwd)/scripts:$PATH\"\n```\n:exclamation: Only the self-compiled HH-suite3 version includes MPI support, since MPI configuration is specific to the local environment.\n\n### Available Databases\nList of available database for HH-suite3: \n  - [Uniclust30](https://uniclust.mmseqs.com) [[pub]](https://doi.org/10.1093/nar/gkw1081)\n  - [BFD](https://bfd.mmseqs.com) (consists of 2.5 billion, mostly enviromental, protein sequences) [[pub]](https://doi.org/10.1038/s41592-019-0437-4)\n  - [Pfam/SCOP/PDB70/dbCAN](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/databases/hhsuite_dbs/)\n\nAlso checkout the [databases (COG/ECOG/CD/...)](http://ftp.tuebingen.mpg.de/pub/protevo/toolkit/databases/hhsuite_dbs) maintained by the [MPI Bioinformatics Toolkit](https://toolkit.tuebingen.mpg.de) [[pub]](https://doi.org/10.1002/cpbi.108).\n\n\n### Compilation\nTo compile from source, you will need a recent C/C++ compiler (at least GCC 4.8 or Clang 3.6) and [CMake](http://cmake.org/) 2.8.12 or later.\n\nTo download the source code and compile the HH-suite execute the following commands:\n```\ngit clone https://github.com/soedinglab/hh-suite.git\nmkdir -p hh-suite/build \u0026\u0026 cd hh-suite/build\ncmake -DCMAKE_INSTALL_PREFIX=. ..\nmake -j 4 \u0026\u0026 make install\nexport PATH=\"$(pwd)/bin:$(pwd)/scripts:$PATH\"\n```\n\n:exclamation: To compile HH-suite3 on macOS, first install the `gcc` compiler from [Homebrew](https://brew.sh). The default macOS `clang` compiler does not support OpenMP and HH-suite3 will only be able to use a single thread. Then replace the `cmake` call above with the following one:\n\n```\nCC=\"$(brew --prefix)/bin/gcc-10\" CXX=\"$(brew --prefix)/bin/g++-10\" cmake -DCMAKE_INSTALL_PREFIX=. ..\n```    \n\n\n## Usage\nFor performing a single search iteration of HHblits, run HHblits with the following command:\n```\nhhblits -i \u003cinput-file\u003e -o \u003cresult-file\u003e -n 1 -d \u003cdatabase-basename\u003e\n```\n\nFor generating an alignment of homologous sequences:\n```\nhhblits -i \u003cinput-file\u003e -o \u003cresult-file\u003e -oa3m \u003cresult-alignment\u003e -d \u003cdatabase-basename\u003e\n```\n\nA detailed list of options for HHblits is available by running HHblits with the `-h` parameter.\n\n## Reference\n\nSteinegger M, Meier M, Mirdita M, Vöhringer H, Haunsberger S J, and Söding J (2019)\nHH-suite3 for fast remote homology detection and deep protein annotation, *BMC Bioinformatics*, 473. [doi: 10.1186/s12859-019-3019-7](https://doi.org/10.1186/s12859-019-3019-7)\n\n## Links\n\n* [Soeding lab](http://www.mpibpc.mpg.de/soeding)\n* [Databases for the HH-suite](http://wwwuser.gwdg.de/~compbiol/data/hhsuite/)\n","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fhh-suite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsoedinglab%2Fhh-suite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsoedinglab%2Fhh-suite/lists"}