{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,27]],"date-time":"2026-10-27T16:10:54Z","timestamp":1793117454763,"version":"4.5.0"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2673,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: Multiple sequence alignments are central to many areas of bioinformatics. It has been shown that the removal of poorly aligned regions from an alignment increases the quality of subsequent analyses. Such an alignment trimming phase is complicated in large-scale phylogenetic analyses that deal with thousands of alignments. Here, we present trimAl, a tool for automated alignment trimming, which is especially suited for large-scale phylogenetic analyses. trimAl can consider several parameters, alone or in multiple combinations, for selecting the most reliable positions in the alignment. These include the proportion of sequences with a gap, the level of amino acid similarity and, if several alignments for the same set of sequences are provided, the level of consistency across different alignments. Moreover, trimAl can automatically select the parameters to be used in each specific alignment so that the signal-to-noise ratio is optimized.<\/jats:p>\n                  <jats:p>Availability: trimAl has been written in C++, it is portable to all platforms. trimAl is freely available for download (http:\/\/trimal.cgenomics.org) and can be used online through the Phylemon web server (http:\/\/phylemon2.bioinfo.cipf.es\/). Supplementary Material is available at http:\/\/trimal.cgenomics.org\/publications.<\/jats:p>\n                  <jats:p>Contact: \u00a0tgabaldon@crg.es<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp348","type":"journal-article","created":{"date-parts":[[2009,6,8]],"date-time":"2009-06-08T20:27:15Z","timestamp":1244492835000},"page":"1972-1973","source":"Crossref","is-referenced-by-count":13237,"title":["trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses"],"prefix":"10.1093","volume":"25","author":[{"given":"Salvador","family":"Capella-Guti\u00e9rrez","sequence":"first","affiliation":[{"name":"Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jos\u00e9 M.","family":"Silla-Mart\u00ednez","sequence":"additional","affiliation":[{"name":"Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"Comparative Genomics group, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader, 88 08003 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2009,6,8]]},"reference":[{"key":"2023013112100340500_B1","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"Castresana","year":"2000","journal-title":"Mol. Biol. Evol."},{"key":"2023013112100340500_B2","doi-asserted-by":"crossref","first-page":"R109","DOI":"10.1186\/gb-2007-8-6-r109","article-title":"The human phylome","volume":"8","author":"Huerta-Cepas","year":"2007","journal-title":"Genome Biol."},{"key":"2023013112100340500_B3","doi-asserted-by":"crossref","first-page":"D491","DOI":"10.1093\/nar\/gkm899","article-title":"PhylomeDB: a database for genome-wide collections of gene phylogenies","volume":"36","author":"Huerta-Cepas","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"2023013112100340500_B4","doi-asserted-by":"crossref","first-page":"e123","DOI":"10.1371\/journal.pcbi.0030123","article-title":"Recent evolutions of multiple sequence alignment algorithms","volume":"3","author":"Notredame","year":"2007","journal-title":"PLoS Comput. Biol."},{"key":"2023013112100340500_B5","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","article-title":"Comparison of phylogenetic trees","volume":"53","author":"Robinson","year":"1981","journal-title":"Math. Biosci."},{"key":"2023013112100340500_B6","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1093\/bioinformatics\/14.2.157","article-title":"Rose: generating sequence families","volume":"14","author":"Stoye","year":"1998","journal-title":"Bioinformatics"},{"key":"2023013112100340500_B7","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1080\/10635150701472164","article-title":"Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments","volume":"56","author":"Talavera","year":"2007","journal-title":"Syst. Biol."},{"key":"2023013112100340500_B8","doi-asserted-by":"crossref","first-page":"W38","DOI":"10.1093\/nar\/gkm224","article-title":"Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics","volume":"35","author":"Tarraga","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"2023013112100340500_B9","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1006\/jmbi.2001.5187","article-title":"Towards a reliable objective function for multiple sequence alignments","volume":"314","author":"Thompson","year":"2001","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1972\/48994574\/bioinformatics_25_15_1972.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/25\/15\/1972\/48994574\/bioinformatics_25_15_1972.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T16:31:24Z","timestamp":1675182684000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/25\/15\/1972\/213148"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,6,8]]},"references-count":9,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2009,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btp348","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2009,8,1]]},"published":{"date-parts":[[2009,6,8]]}}}