{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T12:58:48Z","timestamp":1767963528174,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2017,3,29]],"date-time":"2017-03-29T00:00:00Z","timestamp":1490745600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,7,15]]},"abstract":"Abstract<\/jats:title>\n \n Summary<\/jats:title>\n A number of alignment-free methods have been proposed for phylogeny reconstruction over the past two decades. But there are some long-standing challenges in these methods, including requirement of huge computer memory and CPU time, and existence of duplicate computations. In this article, we address these challenges with the idea of compressed vector, fingerprint and scalable memory management. With these ideas we developed the DLTree algorithm for efficient implementation of the dynamical language model and whole genome-based phylogenetic analysis. The DLTree algorithm was compared with other alignment-free tools, demonstrating that it is more efficient and accurate for phylogeny reconstruction.<\/jats:p>\n <\/jats:sec>\n \n Availability and Implementation<\/jats:title>\n The DLTree algorithm is freely available at http:\/\/dltree.xtu.edu.cn<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btx158","type":"journal-article","created":{"date-parts":[[2017,3,18]],"date-time":"2017-03-18T12:47:27Z","timestamp":1489841247000},"page":"2214-2215","source":"Crossref","is-referenced-by-count":7,"title":["DLTree: efficient and accurate phylogeny reconstruction using the dynamical language method"],"prefix":"10.1093","volume":"33","author":[{"given":"Qi","family":"Wu","sequence":"first","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China"}]},{"given":"Zu-Guo","family":"Yu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Intelligent Computing and Information Processing of Ministry of Education, Hunan Key Laboratory for Computation and Simulation in Science and Engineering, Xiangtan University, Hunan, China"}]},{"given":"Jianyi","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematical Sciences, Nankai University, Tianjin, China"}]}],"member":"286","published-online":{"date-parts":[[2017,3,29]]},"reference":[{"key":"2023051506473533200_btx158-B1","doi-asserted-by":"crossref","first-page":"5155","DOI":"10.1073\/pnas.83.14.5155","article-title":"A measure of the similarity of sets of sequences not requiring sequence alignment","volume":"83","author":"Blaisdell","year":"1986","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023051506473533200_btx158-B2","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1093\/nar\/gks485","article-title":"T-REX: a web server for inferring, validating and visualizing phylogenetic trees and networks","volume":"40","author":"Boc","year":"2012","journal-title":"Nucleic Acids Res"},{"key":"2023051506473533200_btx158-B3","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2148-7-41","article-title":"Whole genome molecular phylogeny of large dsDNA viruses using composition vector method","volume":"7","author":"Gao","year":"2007","journal-title":"BMC Evol. Biol"},{"key":"2023051506473533200_btx158-B4","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1093\/nar\/gku398","article-title":"Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches","volume":"42","author":"Horwege","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"2023051506473533200_btx158-B5","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00239-003-2493-7","article-title":"Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach","volume":"58","author":"Qi","year":"2004","journal-title":"J. Mol. Evol"},{"key":"2023051506473533200_btx158-B6","doi-asserted-by":"crossref","first-page":"2677","DOI":"10.1073\/pnas.0813249106","article-title":"Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions","volume":"106","author":"Sims","year":"2009","journal-title":"Proc. Natl. Acad. Sci. U. S. A"},{"key":"2023051506473533200_btx158-B7","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/5052","article-title":"Genome phylogeny based on gene content","volume":"21","author":"Snel","year":"1999","journal-title":"Nat. Genet"},{"key":"2023051506473533200_btx158-B8","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1093\/bioinformatics\/18.1.100","article-title":"Integrated gene and species phylogenies from unaligned whole genome protein sequences","volume":"18","author":"Stuart","year":"2002","journal-title":"Bioinformatics"},{"key":"2023051506473533200_btx158-B9","doi-asserted-by":"crossref","first-page":"192","DOI":"10.1186\/1471-2148-10-192","article-title":"Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model","volume":"10","author":"Yu","year":"2010","journal-title":"BMC Evol. Biol"},{"key":"2023051506473533200_btx158-B10","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.3390\/ijms11031141","article-title":"Proper distance metrics for phylogenetic analysis using complete genomes without sequence alignment","volume":"11","author":"Yu","year":"2010","journal-title":"Int. J. Mol. Sci"},{"key":"2023051506473533200_btx158-B11","doi-asserted-by":"crossref","first-page":"538","DOI":"10.1007\/s00239-004-0255-9","article-title":"Phylogeny of prokaryotes and chloroplasts revealed by a simple composition approach on all protein sequences from complete genomes without sequence alignment","volume":"60","author":"Yu","year":"2005","journal-title":"J. Mol. Evol"},{"key":"2023051506473533200_btx158-B12","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1016\/j.gpb.2015.08.004","article-title":"CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy","volume":"13","author":"Zuo","year":"2015","journal-title":"Genomics Proteomics Bioinf"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/14\/2214\/50314845\/bioinformatics_33_14_2214.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/14\/2214\/50314845\/bioinformatics_33_14_2214.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,15]],"date-time":"2023-05-15T06:47:51Z","timestamp":1684133271000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/14\/2214\/3091807"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2017,3,29]]},"references-count":12,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2017,7,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx158","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,7,15]]},"published":{"date-parts":[[2017,3,29]]}}}