{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T06:13:06Z","timestamp":1775196786253,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":1466,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/3.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Two methods to add unaligned sequences into an existing multiple sequence alignment have been implemented as the \u2018\u2013add\u2019 and \u2018\u2013addfragments\u2019 options in the MAFFT package. The former option is a basic one and applicable only to full-length sequences, whereas the latter option is applicable even when the unaligned sequences are short and fragmentary. These methods internally infer the phylogenetic relationship among the sequences in the existing alignment and the phylogenetic positions of unaligned sequences. Benchmarks based on two independent simulations consistently suggest that the \u201c\u2013addfragments\u201d option outperforms recent methods, PaPaRa and PAGAN, in accuracy for difficult problems and that these three methods appropriately handle easy problems.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/mafft.cbrc.jp\/alignment\/software\/<\/jats:p>\n               <jats:p>Contact: \u00a0katoh@ifrec.osaka-u.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts578","type":"journal-article","created":{"date-parts":[[2012,10,1]],"date-time":"2012-10-01T00:38:58Z","timestamp":1349051938000},"page":"3144-3146","source":"Crossref","is-referenced-by-count":228,"title":["Adding unaligned sequences into an existing alignment using MAFFT and LAST"],"prefix":"10.1093","volume":"28","author":[{"given":"Kazutaka","family":"Katoh","sequence":"first","affiliation":[]},{"given":"Martin C.","family":"Frith","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2012,9,27]]},"reference":[{"key":"2023062411491797900_bts578-B1","doi-asserted-by":"crossref","first-page":"2068","DOI":"10.1093\/bioinformatics\/btr320","article-title":"Aligning short reads to reference alignments and trees","volume":"27","author":"Berger","year":"2011","journal-title":"Bioinformatics"},{"key":"2023062411491797900_bts578-B2","doi-asserted-by":"crossref","first-page":"D141","DOI":"10.1093\/nar\/gkn879","article-title":"The Ribosomal Database Project: improved alignments and new tools for rRNA analysis","volume":"37","author":"Cole","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"2023062411491797900_bts578-B3","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1007\/BF02603120","article-title":"Progressive sequence alignment as a prerequisite to correct phylogenetic trees","volume":"25","author":"Feng","year":"1987","journal-title":"J. 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