{"id":18613910,"url":"https://github.com/enthought/vpsearch","last_synced_at":"2025-11-03T02:30:39.097Z","repository":{"id":36939063,"uuid":"199520842","full_name":"enthought/vpsearch","owner":"enthought","description":"Fast similarity search for genomic sequences via vantage-point trees","archived":false,"fork":false,"pushed_at":"2023-08-22T01:30:02.000Z","size":130,"stargazers_count":4,"open_issues_count":1,"forks_count":1,"subscribers_count":24,"default_branch":"master","last_synced_at":"2025-01-28T10:47:46.511Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://vpsearch.readthedocs.io/en/latest/","language":"Cython","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/enthought.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES.txt","contributing":"docs/contributing.rst","funding":null,"license":"LICENSE","code_of_conduct":"docs/code_of_conduct.rst","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-07-29T20:14:42.000Z","updated_at":"2023-08-18T05:44:50.000Z","dependencies_parsed_at":"2023-02-10T11:15:53.282Z","dependency_job_id":null,"html_url":"https://github.com/enthought/vpsearch","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/enthought%2Fvpsearch","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/enthought%2Fvpsearch/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/enthought%2Fvpsearch/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/enthought%2Fvpsearch/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/enthought","download_url":"https://codeload.github.com/enthought/vpsearch/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239406446,"owners_count":19633024,"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":[],"created_at":"2024-11-07T03:24:19.707Z","updated_at":"2025-11-03T02:30:39.047Z","avatar_url":"https://github.com/enthought.png","language":"Cython","funding_links":[],"categories":[],"sub_categories":[],"readme":"----------------------------------------------------------------\nvpsearch - Fast Vantage-Point Tree Search for Sequence Databases\n----------------------------------------------------------------\n\n[![PyPI version](https://badge.fury.io/py/vpsearch.svg)](https://badge.fury.io/py/vpsearch)\n![Tests status](https://github.com/enthought/vpsearch/actions/workflows/run-tests.yaml/badge.svg?event=push)\n[![DOI](https://joss.theoj.org/papers/10.21105/joss.04236/status.svg)](https://doi.org/10.21105/joss.04236)\n\nThis is a package for indexing and querying a sequence database for fast\nnearest-neighbor search by means of [vantage point\ntrees](https://en.wikipedia.org/wiki/Vantage-point_tree). For reasonably large\ndatabases, such as [RDP](https://rdp.cme.msu.edu/), this results in sequence\nlookups that are typically 5-10 times faster than other alignment-based lookup\nmethods.\n\nVantage-point tree search uses global-to-global alignment to compare sequences,\nrather than seed-and-extend approximative methods as used for example by\nBLAST.\n\n## Installation and usage\n\nVPsearch can be installed and updated through pip:\n```console\n    pip install -U vpsearch\n```\n\nThis will install a standalone command-line utility `vpsearch` into your\nenvironment, which can be used to build and query a sequence database. For more information on how to do so, see the [documentation](https://vpsearch.readthedocs.io/en/latest/).\n\n## Citing vpsearch\n\nIf you use vpsearch, please cite our paper:\n\n- Joris Vankerschaver, Steven J. Kern, Robert Kern. _VPsearch: fast exact sequence similarity search for genomic sequences_. Journal of Open Source Software, 7(78), 4236, 2002. https://doi.org/10.21105/joss.04236\n\n## License\n\nThis package is licensed under the [3-clause BSD license](LICENSE).\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fenthought%2Fvpsearch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fenthought%2Fvpsearch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fenthought%2Fvpsearch/lists"}