{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T18:03:57Z","timestamp":1775325837852,"version":"3.50.1"},"reference-count":7,"publisher":"Oxford University Press (OUP)","issue":"24","funder":[{"name":"Ministry of Economy and Competitiveness of Spain and FEDER funds of the EU","award":["TIN2013-42148-P"],"award-info":[{"award-number":["TIN2013-42148-P"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,12,15]]},"abstract":"<jats:p>Summary: \u00a0MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. In this work we present MSAProbs-MPI, a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20. Another strong point is that MSAProbs-MPI can deal with large datasets for which MSAProbs and QuickProbs might fail due to time and memory constraints, respectively.<\/jats:p>\n               <jats:p>Availability and Implementation: Source code in C\u2009++\u2009and MPI running on Linux systems as well as a reference manual are available at http:\/\/msaprobs.sourceforge.net<\/jats:p>\n               <jats:p>Contact: \u00a0jgonzalezd@udc.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw558","type":"journal-article","created":{"date-parts":[[2016,9,17]],"date-time":"2016-09-17T02:48:57Z","timestamp":1474080537000},"page":"3826-3828","source":"Crossref","is-referenced-by-count":28,"title":["MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems"],"prefix":"10.1093","volume":"32","author":[{"given":"Jorge","family":"Gonz\u00e1lez-Dom\u00ednguez","sequence":"first","affiliation":[{"name":"1Campus de Elvi\u00f1a, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, 15071 A Coru\u00f1a, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yongchao","family":"Liu","sequence":"additional","affiliation":[{"name":"2School of Computational Science and Engineering, Georgia Institute of Technology, 266 Ferst Drive, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan","family":"Touri\u00f1o","sequence":"additional","affiliation":[{"name":"1Campus de Elvi\u00f1a, Grupo de Arquitectura de Computadores, Universidade da Coru\u00f1a, 15071 A Coru\u00f1a, Spain,"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bertil","family":"Schmidt","sequence":"additional","affiliation":[{"name":"3Institut f\u00fcr Informatik, Johannes Gutenberg Universit\u00e4t Mainz, Staudingerweg 9, Mainz 55128, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2016,8,29]]},"reference":[{"key":"2023020114105995000_btw558-B1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0088901","article-title":"QuickProbs: a fast multiple sequence alignment algorithm designed for graphics processors","volume":"9","author":"Gudy\u015b","year":"2014","journal-title":"PLOS One"},{"key":"2023020114105995000_btw558-B2","doi-asserted-by":"crossref","DOI":"10.1093\/bioinformatics\/btw108","article-title":"A simple method to control over-alignment in the MAFFT multiple sequence alignment program","author":"Katoh","year":"2016","journal-title":"Bioinformatics"},{"key":"2023020114105995000_btw558-B3","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.1093\/bioinformatics\/btq338","article-title":"MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition posterior probabilities","volume":"26","author":"Liu","year":"2010","journal-title":"Bioinformatics"},{"key":"2023020114105995000_btw558-B4","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: a novel method for fast and accurate multiple sequence alignment","volume":"32","author":"Notredame","year":"2000","journal-title":"J. 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