{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,7]],"date-time":"2024-09-07T17:21:25Z","timestamp":1725729685235},"reference-count":44,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2013,4,1]],"date-time":"2013-04-01T00:00:00Z","timestamp":1364774400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"DOI":"10.1186\/1471-2105-14-s7-s4","type":"journal-article","created":{"date-parts":[[2013,4,22]],"date-time":"2013-04-22T10:15:24Z","timestamp":1366625724000},"source":"Crossref","is-referenced-by-count":17,"title":["Alignment-free analysis of barcode sequences by means of compression-based methods"],"prefix":"10.1186","volume":"14","author":[{"given":"Massimo","family":"La Rosa","sequence":"first","affiliation":[]},{"given":"Antonino","family":"Fiannaca","sequence":"additional","affiliation":[]},{"given":"Riccardo","family":"Rizzo","sequence":"additional","affiliation":[]},{"given":"Alfonso","family":"Urso","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,22]]},"reference":[{"issue":"12","key":"5814_CR1","doi-asserted-by":"publisher","first-page":"4775","DOI":"10.1073\/pnas.0700466104","volume":"104","author":"SE Miller","year":"2007","unstructured":"Miller SE: DNA barcoding and the renaissance of taxonomy. Proceedings of the National Academy of Sciences of the United States of America. 2007, 104 (12): 4775-4776. 10.1073\/pnas.0700466104.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"1512","key":"5814_CR2","doi-asserted-by":"publisher","first-page":"313","DOI":"10.1098\/rspb.2002.2218","volume":"270","author":"PDN Hebert","year":"2003","unstructured":"Hebert PDN, Cywinska A, Ball SL, DeWaard JR: Biological identifications through DNA barcodes. Proceedings of the Royal Society. Series B, Biological sciences. 2003, 270 (1512): 313-321. 10.1098\/rspb.2002.2218.","journal-title":"Proceedings of the Royal Society. Series B, Biological sciences"},{"issue":"1462","key":"5814_CR3","doi-asserted-by":"publisher","first-page":"1805","DOI":"10.1098\/rstb.2005.1730","volume":"360","author":"V Savolainen","year":"2005","unstructured":"Savolainen V, Cowan RS, Vogler AP, Roderick GK, Lane R: Towards writing the encyclopedia of life: an introduction to DNA barcoding. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2005, 360 (1462): 1805-1811. 10.1098\/rstb.2005.1730.","journal-title":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences"},{"issue":"Suppl","key":"5814_CR4","doi-asserted-by":"publisher","first-page":"S96","DOI":"10.1098\/rsbl.2003.0025","volume":"270","author":"PDN Hebert","year":"2003","unstructured":"Hebert PDN, Ratnasingham S, DeWaard JR: Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society. Series B, Biological sciences. 2003, 270 (Suppl): S96-S99. 10.1098\/rsbl.2003.0025.","journal-title":"Proceedings of the Royal Society. Series B, Biological sciences"},{"issue":"1462","key":"5814_CR5","doi-asserted-by":"publisher","first-page":"1847","DOI":"10.1098\/rstb.2005.1716","volume":"360","author":"RD Ward","year":"2005","unstructured":"Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PDN: DNA barcoding Australia's fish species. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2005, 360 (1462): 1847-1857. 10.1098\/rstb.2005.1716.","journal-title":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences"},{"key":"5814_CR6","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1186\/1746-5354-3-2-52","volume":"3","author":"F Costa","year":"2007","unstructured":"Costa F, Carvahlo G: The Barcode of Life Initiative: synopsis and prospective societal impacts of DNA barcoding of fish. Genomics, Society and Policy. 2007, 3: 29-40.","journal-title":"Genomics, Society and Policy"},{"issue":"10","key":"5814_CR7","doi-asserted-by":"publisher","first-page":"1657","DOI":"10.1371\/journal.pbio.0020312","volume":"2","author":"PDN Hebert","year":"2004","unstructured":"Hebert PDN, Stoeckle MY, Zemlak TS, Francis CM: Identification of Birds through DNA Barcodes. PLoS biology. 2004, 2 (10): 1657-1663.","journal-title":"PLoS biology"},{"issue":"1462","key":"5814_CR8","doi-asserted-by":"publisher","first-page":"1825","DOI":"10.1098\/rstb.2005.1714","volume":"360","author":"MA Smith","year":"2005","unstructured":"Smith MA, Fisher BL, Hebert PDN: DNA barcoding for effective biodiversity assessment of a hyperdiverse arthropod group: the ants of Madagascar. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 2005, 360 (1462): 1825-1834. 10.1098\/rstb.2005.1714.","journal-title":"Philosophical transactions of the Royal Society of London. Series B, Biological sciences"},{"issue":"10","key":"5814_CR9","doi-asserted-by":"publisher","first-page":"3657","DOI":"10.1073\/pnas.0511318103","volume":"103","author":"MA Smith","year":"2006","unstructured":"Smith MA, Woodley NE, Janzen DH, Hallwachs W, Hebert PDN: DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). Proceedings of the National Academy of Sciences of the United States of America. 2006, 103 (10): 3657-3662. 10.1073\/pnas.0511318103.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"5814_CR10","doi-asserted-by":"publisher","first-page":"968","DOI":"10.1073\/pnas.0510466103","volume":"103","author":"M Hajibabaei","year":"2006","unstructured":"Hajibabaei M, Janzen DH, Burns JM, Hallwachs W, Hebert PDN: DNA barcodes distinguish species of tropical Lepidoptera. Proceedings of the National Academy of Sciences of the United States of America. 2006, 103 (4): 968-971. 10.1073\/pnas.0510466103.","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"4","key":"5814_CR11","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou N, Nei M: The Neighbor-Joining Method: a new method for reconstructing phylogenetic trees. Molecular biology and evolution. 1987, 4 (4): 406-425.","journal-title":"Molecular biology and evolution"},{"issue":"4","key":"5814_CR12","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.tig.2007.02.001","volume":"23","author":"M Hajibabaei","year":"2007","unstructured":"Hajibabaei M, Singer GaC, Hebert PDN, Hickey Da: DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics. Trends in genetics. 2007, 23 (4): 167-172. 10.1016\/j.tig.2007.02.001.","journal-title":"Trends in genetics"},{"key":"5814_CR13","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780195135848.001.0001","volume-title":"Molecular Evolution and Phylogenetics","author":"M Nei","year":"2000","unstructured":"Nei M, Kumar M: Molecular Evolution and Phylogenetics. 2000, New York: Oxford University Press"},{"issue":"12","key":"5814_CR14","doi-asserted-by":"publisher","first-page":"3250","DOI":"10.1109\/TIT.2004.838101","volume":"50","author":"M Li","year":"2004","unstructured":"Li M, Chen X, Li X: The similarity metric. IEEE Transactions on Information Theory. 2004, 50 (12): 3250-3264. 10.1109\/TIT.2004.838101.","journal-title":"IEEE Transactions on Information Theory"},{"key":"5814_CR15","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-2606-0","volume-title":"An Introduction to Kolmogorov Complexity and its Applications","author":"M Li","year":"1997","unstructured":"Li M, Vitanyi P: An Introduction to Kolmogorov Complexity and its Applications. 1997, New York: Springer"},{"issue":"4","key":"5814_CR16","doi-asserted-by":"publisher","first-page":"1523","DOI":"10.1109\/TIT.2005.844059","volume":"51","author":"R Cilibrasi","year":"2005","unstructured":"Cilibrasi R, Vit\u00e1nyi P: Clustering by compression. IEEE Transactions on Information Theory. 2005, 51 (4): 1523-1545. 10.1109\/TIT.2005.844059.","journal-title":"IEEE Transactions on Information Theory"},{"issue":"2","key":"5814_CR17","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1093\/bioinformatics\/17.2.149","volume":"17","author":"M Li","year":"2001","unstructured":"Li M, Badger J, Chen X, Kwong S: An information-based sequence distance and its application to whole mitochondrial genome phylogeny. Bioinformatics. 2001, 17 (2): 149-154. 10.1093\/bioinformatics\/17.2.149.","journal-title":"Bioinformatics"},{"key":"5814_CR18","doi-asserted-by":"crossref","unstructured":"Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment. BMC Bioinformatics. 2007, 8 (252):","DOI":"10.1186\/1471-2105-8-252"},{"key":"5814_CR19","volume-title":"Information Retrieval","author":"C van Rijsbergen","year":"1979","unstructured":"van Rijsbergen C: Information Retrieval. 1979, London"},{"key":"5814_CR20","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1016\/0025-5564(81)90043-2","volume":"53","author":"D Robinson","year":"1981","unstructured":"Robinson D, Foulds L: Comparison of phylogenetic trees. Mathematical Biosciences. 1981, 53: 131-147. 10.1016\/0025-5564(81)90043-2.","journal-title":"Mathematical Biosciences"},{"key":"5814_CR21","doi-asserted-by":"publisher","first-page":"740","DOI":"10.1007\/978-3-540-85567-5_92","volume-title":"Knowledge-Based Intelligent Information and Engineering Systems","author":"M La Rosa","year":"2008","unstructured":"La Rosa M, Rizzo R, Urso A, Gaglio S: Comparison of genomic sequences clustering using normalized compression distance and evolutionary distance. Knowledge-Based Intelligent Information and Engineering Systems. 2008, Springer, 740-746."},{"issue":"4","key":"5814_CR22","doi-asserted-by":"publisher","first-page":"345","DOI":"10.1504\/IJKESDP.2009.028987","volume":"1","author":"M La Rosa","year":"2009","unstructured":"La Rosa M, Gaglio S, Rizzo R, Urso A: Normalised compression distance and evolutionary distance of genomic sequences: comparison of clustering results. International Journal of Knowledge Engineering and Soft Data Paradigms. 2009, 1 (4): 345-362. 10.1504\/IJKESDP.2009.028987.","journal-title":"International Journal of Knowledge Engineering and Soft Data Paradigms"},{"key":"5814_CR23","volume-title":"Proceedings of 2012 Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 1","author":"A Fiannaca","year":"2012","unstructured":"Fiannaca A, La Rosa M, Rizzo R, Urso A: A Study of Compression-Based Methods for the Analysis of Barcode Sequences. Proceedings of 2012 Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB), 1. 2012"},{"key":"5814_CR24","volume-title":"Molecular Ecology Notes","author":"R Ratnasingham","year":"2007","unstructured":"Ratnasingham R, Hebert P: BOLD: The Barcode of Life Data System. Molecular Ecology Notes. 2007"},{"issue":"4","key":"5814_CR25","doi-asserted-by":"publisher","first-page":"1407","DOI":"10.1109\/18.681318","volume":"44","author":"C Bennett","year":"1998","unstructured":"Bennett C, G\u00e1cs P, Li M, Vit\u00e1nyi P, Zurek W: Information Distance. IEEE Transactions on Information Theory. 1998, 44 (4): 1407-1423.","journal-title":"IEEE Transactions on Information Theory"},{"key":"5814_CR26","first-page":"61","volume-title":"IEEE Engineering in Medicine and Biology","author":"X Chen","year":"2001","unstructured":"Chen X, Kwong S, Li M: A compression algorithm for DNA sequences. IEEE Engineering in Medicine and Biology. 2001, 61-66. (August)"},{"issue":"3","key":"5814_CR27","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1109\/TIT.1977.1055714","volume":"23","author":"J Ziv","year":"1977","unstructured":"Ziv J, Lempel A: A universal algorithm for sequential data compression. IEEE Transactions on Information Theory. 1977, 23 (3): 337-343. 10.1109\/TIT.1977.1055714.","journal-title":"IEEE Transactions on Information Theory"},{"key":"5814_CR28","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1073\/pnas.78.1.454","volume":"78","author":"M Kimura","year":"1981","unstructured":"Kimura M: Estimation of evolutionary distances between homologous nucleotide sequences. Proceedings of the National Academy of Sciences. 1981, 78: 454-458. 10.1073\/pnas.78.1.454.","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"5814_CR29","first-page":"269","volume":"1","author":"F Tajima","year":"1984","unstructured":"Tajima F, Nei M: Estimation of evolutionary distance between nucleotide sequences. Molecular biology and evolution. 1984, 1: 269-285.","journal-title":"Molecular biology and evolution"},{"key":"5814_CR30","first-page":"678","volume":"9","author":"K Tamura","year":"1992","unstructured":"Tamura K: Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution. 1992, 9: 678-687.","journal-title":"Molecular Biology and Evolution"},{"key":"5814_CR31","first-page":"512","volume":"10","author":"F Tamura","year":"1993","unstructured":"Tamura F, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Molecular biology and evolution. 1993, 10: 512-526.","journal-title":"Molecular biology and evolution"},{"key":"5814_CR32","doi-asserted-by":"publisher","first-page":"11030","DOI":"10.1073\/pnas.0404206101","volume":"101","author":"F Tamura","year":"2004","unstructured":"Tamura F, Nei M, Kumar M: Prospects for inferring very large phylogenies by using the neighbor-joining method. Proceedings of the National Academy of Sciences. 2004, 101: 11030-11035. 10.1073\/pnas.0404206101.","journal-title":"Proceedings of the National Academy of Sciences"},{"key":"5814_CR33","doi-asserted-by":"publisher","DOI":"10.1016\/B978-1-4832-3211-9.50009-7","volume-title":"Evolution of protein molecules","author":"T Jukes","year":"1969","unstructured":"Jukes T, Cantor C: Evolution of protein molecules. 1969, New York: Academic Press"},{"issue":"10","key":"5814_CR34","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S: MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Molecular biology and evolution. 2011, 28 (10): 2731-2739. 10.1093\/molbev\/msr121.","journal-title":"Molecular biology and evolution"},{"key":"5814_CR35","doi-asserted-by":"publisher","first-page":"61","DOI":"10.1016\/S1874-5334(06)80006-7","volume":"6","author":"V Makarenkov","year":"2006","unstructured":"Makarenkov V, Kevorkov D, Legendre P: Phylogenetic network construction approaches. Applied Mycology and Biotechnology. 2006, 6: 61-97.","journal-title":"Applied Mycology and Biotechnology"},{"key":"5814_CR36","volume-title":"Numerical Taxonomy: The Principles and Practice of Numerical Classification","author":"PH Sneath","year":"1973","unstructured":"Sneath PH, Sokal RR: Numerical Taxonomy: The Principles and Practice of Numerical Classification. 1973, San Francisco: W.H. Freeman"},{"key":"5814_CR37","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1093\/bioinformatics\/bti720","volume":"22","author":"TMW Nye","year":"2006","unstructured":"Nye TMW, Li\u00f2 P, Gilks WR: A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics. 2006, 22: 117-119. 10.1093\/bioinformatics\/bti720.","journal-title":"Bioinformatics"},{"key":"5814_CR38","doi-asserted-by":"publisher","first-page":"e30490","DOI":"10.1371\/journal.pone.0030490","volume":"7","author":"R van Velzen","year":"2012","unstructured":"van Velzen R, Weitschek E, Felici G, Bakker FT: DNA barcoding of recently diverged species: relative performance of matching methods. PloS one. 2012, 7: e30490-10.1371\/journal.pone.0030490.","journal-title":"PloS one"},{"issue":"2","key":"5814_CR39","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1080\/10635150802032990","volume":"57","author":"Ha Ross","year":"2008","unstructured":"Ross Ha, Murugan S, Li WLS: Testing the reliability of genetic methods of species identification via simulation. Systematic biology. 2008, 57 (2): 216-30. 10.1080\/10635150802032990.","journal-title":"Systematic biology"},{"key":"5814_CR40","volume-title":"Mesquite: a modular system for evolutionary analysis","author":"W Maddison","year":"2011","unstructured":"Maddison W, Maddison D: Mesquite: a modular system for evolutionary analysis. 2011, [ http:\/\/mesquiteproject.org ]"},{"key":"5814_CR41","doi-asserted-by":"publisher","first-page":"91","DOI":"10.1016\/S0025-5564(00)00061-4","volume":"170","author":"M Steel","year":"2001","unstructured":"Steel M, McKenzie A: Properties of phylogenetic trees generated by Yule-type speciation models. Mathematical Biosciences. 2001, 170: 91-112. 10.1016\/S0025-5564(00)00061-4.","journal-title":"Mathematical Biosciences"},{"issue":"3","key":"5814_CR42","first-page":"235","volume":"13","author":"A Rambaut","year":"1997","unstructured":"Rambaut A, Grassly N: Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 1997, 13 (3): 235-38.","journal-title":"Comput Appl Biosci"},{"issue":"2","key":"5814_CR43","doi-asserted-by":"publisher","first-page":"160","DOI":"10.1007\/BF02101694","volume":"22","author":"M Hasegawa","year":"1985","unstructured":"Hasegawa M, Kishino H, Yano T: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of molecular evolution. 1985, 22 (2): 160-74. 10.1007\/BF02101694.","journal-title":"Journal of molecular evolution"},{"key":"5814_CR44","first-page":"590","volume-title":"Parallel and Distributed Processing Symposium","author":"K Chaichoompu","year":"2006","unstructured":"Chaichoompu K, Kittitornkun S, Tongsima S: MT-ClustalW: multithreading multiple sequence alignment. Parallel and Distributed Processing Symposium. 2006, 590-594."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S7-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S7-S4\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S7-S4.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,9]],"date-time":"2024-05-09T10:05:05Z","timestamp":1715249105000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S7-S4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":44,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["5814"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s7-s4","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,4]]},"article-number":"S4"}}