{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,7]],"date-time":"2025-05-07T07:35:30Z","timestamp":1746603330878},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,4,15]]},"abstract":"Abstract<\/jats:title>\n Summary: Unipro UGENE is a multiplatform open-source software with the main goal of assisting molecular biologists without much expertise in bioinformatics to manage, analyze and visualize their data. UGENE integrates widely used bioinformatics tools within a common user interface. The toolkit supports multiple biological data formats and allows the retrieval of data from remote data sources. It provides visualization modules for biological objects such as annotated genome sequences, Next Generation Sequencing (NGS) assembly data, multiple sequence alignments, phylogenetic trees and 3D structures. Most of the integrated algorithms are tuned for maximum performance by the usage of multithreading and special processor instructions. UGENE includes a visual environment for creating reusable workflows that can be launched on local resources or in a High Performance Computing (HPC) environment. UGENE is written in C++ using the Qt framework. The built-in plugin system and structured UGENE API make it possible to extend the toolkit with new functionality.<\/jats:p>\n Availability and implementation: UGENE binaries are freely available for MS Windows, Linux and Mac OS X at http:\/\/ugene.unipro.ru\/download.html. UGENE code is licensed under the GPLv2; the information about the code licensing and copyright of integrated tools can be found in the LICENSE.3rd_party file provided with the source bundle.<\/jats:p>\n Contact: \u00a0ugene@unipro.ru<\/jats:p>\n Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts091","type":"journal-article","created":{"date-parts":[[2012,2,25]],"date-time":"2012-02-25T03:45:12Z","timestamp":1330141512000},"page":"1166-1167","source":"Crossref","is-referenced-by-count":2353,"title":["Unipro UGENE: a unified bioinformatics toolkit"],"prefix":"10.1093","volume":"28","author":[{"given":"Konstantin","family":"Okonechnikov","sequence":"first","affiliation":[]},{"given":"Olga","family":"Golosova","sequence":"additional","affiliation":[]},{"given":"Mikhail","family":"Fursov","sequence":"additional","affiliation":[]},{"name":"the UGENE team","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,2,24]]},"reference":[{"key":"2023012711533390800_B1","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012711533390800_B2","doi-asserted-by":"crossref","first-page":"R86","DOI":"10.1186\/gb-2010-11-8-r86","article-title":"Galaxy: a comprehensive approach for supporting accessible, reproducible and transparent research in the life sciences","volume":"11","author":"Goecks","year":"2010","journal-title":"Genome Biol."},{"key":"2023012711533390800_B3","doi-asserted-by":"crossref","first-page":"W729","DOI":"10.1093\/nar\/gkl320","article-title":"Taverna: a tool for building and running workflows of services","volume":"34","author":"Hull","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012711533390800_B4","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012711533390800_B5","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1093\/bib\/3.3.296","article-title":"The Bio* Toolkits\u2014a brief overview","volume":"3","author":"Mangalam","year":"2002","journal-title":"Brief. 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