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The quality of alignment will affect downstream analysis. MAFFT has adopted the Fast Fourier Transform method for searching the homologous segments and using them as anchors to divide the sequences, then making alignment only on segments, which can save time and memory without overly reducing the sequence alignment quality. MAFFT becomes slow when the dataset is large.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We made a software, WMSA, which uses the divide-and-conquer method to split the sequences into clusters, aligns those clusters into profiles with the center star strategy and then makes a progressive profile\u2013profile alignment. The alignment is conducted by the compiled algorithms of MAFFT, K-Band with multithread parallelism. Our method can balance time, space and quality and performs better than MAFFT in test experiments on highly conserved datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code is freely available at https:\/\/github.com\/malabz\/WMSA\/, which is implemented in C\/C++ and supported on Linux, and datasets are available at https:\/\/github.com\/malabz\/WMSA-dataset.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac658","type":"journal-article","created":{"date-parts":[[2022,9,29]],"date-time":"2022-09-29T20:48:12Z","timestamp":1664484492000},"page":"5019-5025","source":"Crossref","is-referenced-by-count":21,"title":["WMSA: a novel method for multiple sequence alignment of DNA sequences"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4843-3350","authenticated-orcid":false,"given":"Yanming","family":"Wei","sequence":"first","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , Xi\u2019an, Shaanxi 710071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China , Quzhou, Zhejiang 324003, China"},{"name":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China , Chengdu, Sichuan 610054, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Furong","family":"Tang","sequence":"additional","affiliation":[{"name":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China , Quzhou, Zhejiang 324003, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8351-3332","authenticated-orcid":false,"given":"Liang","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Technology, Xidian University , Xi\u2019an, Shaanxi 710071, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,30]]},"reference":[{"key":"2022112014190981200_btac658-B1","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1145\/3317550.3321435","volume-title":"Proceedings of the Workshop on Hot Topics in Operating Systems","author":"Baumann","year":"2019"},{"key":"2022112014190981200_btac658-B2","doi-asserted-by":"crossref","first-page":"33964","DOI":"10.1038\/srep33964","article-title":"FAMSA: fast and accurate multiple sequence alignment of huge protein families","volume":"6","author":"Deorowicz","year":"2016","journal-title":"Sci. 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