{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T15:23:20Z","timestamp":1768577000551,"version":"3.49.0"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Clearcut is an open source implementation for the relaxed neighbor joining (RNJ) algorithm. While traditional neighbor joining (NJ) remains a popular method for distance-based phylogenetic tree reconstruction, it suffers from a O(N3) time complexity, where N represents the number of taxa in the input. Due to this steep asymptotic time complexity, NJ cannot reasonably handle very large datasets. In contrast, RNJ realizes a typical-case time complexity on the order of N2logN without any significant qualitative difference in output. RNJ is particularly useful when inferring a very large tree or a large number of trees. In addition, RNJ retains the desirable property that it will always reconstruct the true tree given a matrix of additive pairwise distances. Clearcut implements RNJ as a C program, which takes either a set of aligned sequences or a pre-computed distance matrix as input and produces a phylogenetic tree. Alternatively, Clearcut can reconstruct phylogenies using an extremely fast standard NJ implementation.<\/jats:p>\n               <jats:p>Availability: Clearcut source code is available for download at:<\/jats:p>\n               <jats:p>Contact: \u00a0sheneman@hungry.com<\/jats:p>\n               <jats:p>Supplementary information: \u00a0<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl478","type":"journal-article","created":{"date-parts":[[2006,9,19]],"date-time":"2006-09-19T00:42:24Z","timestamp":1158626544000},"page":"2823-2824","source":"Crossref","is-referenced-by-count":160,"title":["Clearcut: a fast implementation of relaxed neighbor joining"],"prefix":"10.1093","volume":"22","author":[{"given":"Luke","family":"Sheneman","sequence":"first","affiliation":[{"name":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason","family":"Evans","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James A.","family":"Foster","sequence":"additional","affiliation":[{"name":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,9,18]]},"reference":[{"key":"2023012408421922600_b1","doi-asserted-by":"crossref","first-page":"D294","DOI":"10.1093\/nar\/gki038","article-title":"The ribosomal database project (RDP-II): sequences and tools for high-throughput rRNA analysis","volume":"33","author":"Cole","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012408421922600_b2","first-page":"127","article-title":"Graphviz and dynagraph\u2014static and dynamic graph drawing tools","volume-title":"Graph Drawing Software","author":"Ellson","year":"2003"},{"key":"2023012408421922600_b3","doi-asserted-by":"crossref","first-page":"785","DOI":"10.1007\/s00239-005-0176-2","article-title":"Relaxed neighbor-joining: a fast distance-based phylogenetic tree construction method","volume":"62","author":"Evans","year":"2006","journal-title":"J. Mol. Evol."},{"key":"2023012408421922600_b4","article-title":"PHYLIP (phylogeny inference package) version 3.6","author":"Felsenstein","year":"2004"},{"key":"2023012408421922600_b5","doi-asserted-by":"crossref","first-page":"1546","DOI":"10.1093\/bioinformatics\/18.11.1546","article-title":"QuickTree: building huge neighbour-joining trees of protein sequences","volume":"18","author":"Howe","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012408421922600_b6","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1016\/B978-1-4832-3211-9.50009-7","article-title":"Evolution of protein molecules","volume-title":"Mammalian Protein Metabolism, chapter 24","author":"Jukes","year":"1969"},{"key":"2023012408421922600_b7","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1007\/BF01731581","article-title":"A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences","volume":"16","author":"Kimura","year":"1980","journal-title":"J. Mol. Evol."},{"key":"2023012408421922600_b8","doi-asserted-by":"crossref","first-page":"3261","DOI":"10.1093\/bioinformatics\/bth359","article-title":"QuickJoin\u2014fast neighbour-joining tree reconstruction","volume":"20","author":"Mailund","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408421922600_b9","first-page":"406","article-title":"The neighbor-joining method: a new method for reconstructing phylogenetic trees","volume":"4","author":"Saitou","year":"1987","journal-title":"Mol. Biol. Evol."},{"key":"2023012408421922600_b10","first-page":"729","article-title":"A note on the neighbor-joining algorithm of Saitou and Nei","volume":"5","author":"Studier","year":"1988","journal-title":"Mol. Biol. Evol."},{"key":"2023012408421922600_b11","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/0022-5193(77)90351-4","article-title":"Additive evolutionary trees","volume":"64","author":"Waterman","year":"1977","journal-title":"J. Theor. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/22\/2823\/48838165\/bioinformatics_22_22_2823.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/22\/2823\/48838165\/bioinformatics_22_22_2823.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T09:00:58Z","timestamp":1674550858000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/22\/2823\/197536"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,9,18]]},"references-count":11,"journal-issue":{"issue":"22","published-print":{"date-parts":[[2006,11,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl478","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,11,15]]},"published":{"date-parts":[[2006,9,18]]}}}