{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T09:58:08Z","timestamp":1780394288121,"version":"3.54.1"},"update-to":[{"DOI":"10.1371\/journal.pcbi.1008950","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2021,10,18]],"date-time":"2021-10-18T00:00:00Z","timestamp":1634515200000}}],"reference-count":20,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2021,10,6]],"date-time":"2021-10-06T00:00:00Z","timestamp":1633478400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Debra & Ira Cohen Graduate Fellowship"},{"name":"Research Assistantship from Dr. Tandy Warnow, funded by NSF grant","award":["ABI-1458652"],"award-info":[{"award-number":["ABI-1458652"]}]}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"abstract":"<jats:p>\n                    Multiple sequence alignment tools struggle to keep pace with rapidly growing sequence data, as few methods can handle large datasets while maintaining alignment accuracy. We recently introduced MAGUS, a new state-of-the-art method for aligning large numbers of sequences. In this paper, we present a comprehensive set of enhancements that allow MAGUS to align vastly larger datasets with greater speed. We compare MAGUS to other leading alignment methods on datasets of up to one million sequences. Our results demonstrate the advantages of MAGUS over other alignment software in both accuracy and speed. MAGUS is freely available in open-source form at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/vlasmirnov\/MAGUS\" xlink:type=\"simple\">https:\/\/github.com\/vlasmirnov\/MAGUS<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1371\/journal.pcbi.1008950","type":"journal-article","created":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T08:23:48Z","timestamp":1633595028000},"page":"e1008950","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":13,"title":["Recursive MAGUS: Scalable and accurate multiple sequence alignment"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7826-1214","authenticated-orcid":true,"given":"Vladimir","family":"Smirnov","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,10,6]]},"reference":[{"issue":"1","key":"pcbi.1008950.ref001","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-5-113","article-title":"MUSCLE: a multiple sequence alignment method with reduced time and space complexity","volume":"5","author":"RC Edgar","year":"2004","journal-title":"BMC bioinformatics"},{"issue":"1","key":"pcbi.1008950.ref002","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/msb.2011.75","article-title":"Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega","volume":"7","author":"F Sievers","year":"2011","journal-title":"Molecular systems biology"},{"issue":"2","key":"pcbi.1008950.ref003","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1093\/nar\/gki198","article-title":"MAFFT version 5: improvement in accuracy of multiple sequence alignment","volume":"33","author":"K Katoh","year":"2005","journal-title":"Nucleic acids research"},{"issue":"1","key":"pcbi.1008950.ref004","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1186\/s13059-015-0688-z","article-title":"Ultra-large alignments using phylogeny-aware profiles","volume":"16","author":"NpD Nguyen","year":"2015","journal-title":"Genome Biology"},{"issue":"6","key":"pcbi.1008950.ref005","first-page":"1928","article-title":"Kalign 3: multiple sequence alignment of large datasets","volume":"36","author":"T Lassmann","year":"2019","journal-title":"Bioinf"},{"issue":"1","key":"pcbi.1008950.ref006","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":"302","author":"C Notredame","year":"2000","journal-title":"Journal of molecular biology"},{"issue":"2","key":"pcbi.1008950.ref007","doi-asserted-by":"crossref","first-page":"330","DOI":"10.1101\/gr.2821705","article-title":"ProbCons: Probabilistic consistency-based multiple sequence alignment","volume":"15","author":"CB Do","year":"2005","journal-title":"Genome research"},{"issue":"7","key":"pcbi.1008950.ref008","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1093\/bioinformatics\/btm017","article-title":"PROMALS: towards accurate multiple sequence alignments of distantly related proteins","volume":"23","author":"J Pei","year":"2007","journal-title":"Bioinf"},{"issue":"5934","key":"pcbi.1008950.ref009","doi-asserted-by":"crossref","first-page":"1561","DOI":"10.1126\/science.1171243","article-title":"Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees","volume":"324","author":"K Liu","year":"2009","journal-title":"Science"},{"issue":"1","key":"pcbi.1008950.ref010","doi-asserted-by":"crossref","first-page":"90","DOI":"10.1093\/sysbio\/syr095","article-title":"SATe-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees","volume":"61","author":"K Liu","year":"2012","journal-title":"Systematic biology"},{"issue":"5","key":"pcbi.1008950.ref011","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1089\/cmb.2014.0156","article-title":"PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences","volume":"22","author":"S Mirarab","year":"2015","journal-title":"Journal of Computational Biology"},{"key":"pcbi.1008950.ref012","article-title":"MAGUS: Multiple Sequence Alignment using Graph Clustering","author":"V Smirnov","year":"2020","journal-title":"Bioinformatics"},{"key":"pcbi.1008950.ref013","unstructured":"Van Dongen SM. A cluster algorithm for graphs. Amsterdam: National Research Institute for Mathematics and Computer Science in the Netherlands; 2000. Available from: https:\/\/ir.cwi.nl\/pub\/4463."},{"issue":"3","key":"pcbi.1008950.ref014","doi-asserted-by":"crossref","first-page":"e9490","DOI":"10.1371\/journal.pone.0009490","article-title":"FastTree 2\u2013approximately maximum-likelihood trees for large alignments","volume":"5","author":"MN Price","year":"2010","journal-title":"PloS one"},{"key":"pcbi.1008950.ref015","unstructured":"Eddy SR. HMMER website; 2020. 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