{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,30]],"date-time":"2026-05-30T03:09:55Z","timestamp":1780110595556,"version":"3.54.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Multiple sequence alignment (MSA) is a central tool in most modern biology studies. However, despite generations of valuable tools, human experts are still able to improve automatically generated MSAs. In an effort to automatically identify the most reliable MSA for a given protein family, we propose a very simple protocol, named AQUA for \u2018Automated quality improvement for multiple sequence alignments\u2019. Our current implementation relies on two alignment programs (MUSCLE and MAFFT), one refinement program (RASCAL) and one assessment program (NORMD), but other programs could be incorporated at any of the three steps.<\/jats:p>\n               <jats:p>Availability: AQUA is implemented in Tcl\/Tk and runs in command line on all platforms. The source code is available under the GNU GPL license. Source code, README and Supplementary data are available at http:\/\/www.bork.embl.de\/Docu\/AQUA.<\/jats:p>\n               <jats:p>Contact: \u00a0muller@embl.de, bork@embl.de<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp651","type":"journal-article","created":{"date-parts":[[2009,11,20]],"date-time":"2009-11-20T02:22:18Z","timestamp":1258683738000},"page":"263-265","source":"Crossref","is-referenced-by-count":51,"title":["AQUA: automated quality improvement for multiple sequence alignments"],"prefix":"10.1093","volume":"26","author":[{"given":"Jean","family":"Muller","sequence":"first","affiliation":[{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher J.","family":"Creevey","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Julie D.","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Detlev","family":"Arendt","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peer","family":"Bork","sequence":"additional","affiliation":[{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"},{"name":"1 European Molecular Biology Laboratory, Meyerhofstrasse 1, 69012 Heidelberg, Germany, 2 D\u00e9partement de Biologie et G\u00e9nomique Structurales, Institut de G\u00e9n\u00e9tique et de Biologie Mol\u00e9culaire et Cellulaire, (CNRS\/INSERM\/ULP), BP 10142, 67404 Illkirch Cedex and 3 Max-Delbr\u00fcck-Centre for Molecular Medicine, Robert-R\u00f6ssle-Strasse 10, 13092 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,11,19]]},"reference":[{"key":"2023012508214991700_B1","doi-asserted-by":"crossref","first-page":"W604","DOI":"10.1093\/nar\/gkl092","article-title":"Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee","volume":"34","author":"Armougom","year":"2006","journal-title":"Nucleic Acids 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