{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T06:43:05Z","timestamp":1791182585696,"version":"4.1.0"},"reference-count":66,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2014,10,5]],"date-time":"2014-10-05T00:00:00Z","timestamp":1412467200000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Genet"],"published-print":{"date-parts":[[2014,11]]},"DOI":"10.1038\/ng.3114","type":"journal-article","created":{"date-parts":[[2014,10,5]],"date-time":"2014-10-05T19:51:08Z","timestamp":1412538668000},"page":"1205-1211","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":86,"title":["Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates"],"prefix":"10.1038","volume":"46","author":[{"given":"Leonor","family":"S\u00e1nchez-Bus\u00f3","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"I\u00f1aki","family":"Comas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guillermo","family":"Jorques","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0879-5798","authenticated-orcid":false,"given":"Fernando","family":"Gonz\u00e1lez-Candelas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2014,10,5]]},"reference":[{"key":"BFng3114_CR1","unstructured":"Lawrence, J.G. & Retchless, A.C. in Horizontal Gene Transfer: Genomes in Flux (eds. Gogarten, M.B., Gogarten, J.P. & Olendzenski, L.) 29\u201353 (Humana Press, New York, 2009)."},{"key":"BFng3114_CR2","doi-asserted-by":"publisher","first-page":"e1000601","DOI":"10.1371\/journal.pgen.1000601","volume":"5","author":"BR Levin","year":"2009","unstructured":"Levin, B.R. & Cornejo, O.E. The population and evolutionary dynamics of homologous gene recombination in bacteria. PLoS Genet. 5, e1000601 (2009).","journal-title":"PLoS Genet."},{"key":"BFng3114_CR3","doi-asserted-by":"publisher","first-page":"27","DOI":"10.3389\/fmicb.2012.00027","volume":"3","author":"JP Townsend","year":"2012","unstructured":"Townsend, J.P., B\u00f8hn, T. & Nielsen, K.M. Assessing the probability of detection of horizontal gene transfer events in bacterial populations. Front. Microbiol. 3, 27 (2012).","journal-title":"Front. Microbiol."},{"key":"BFng3114_CR4","doi-asserted-by":"publisher","first-page":"6981","DOI":"10.1073\/pnas.97.13.6981","volume":"97","author":"BR Levin","year":"2000","unstructured":"Levin, B.R. & Bergstrom, C.T. Bacteria are different: observations, interpretations, speculations, and opinions about the mechanisms of adaptive evolution in prokaryotes. Proc. Natl. Acad. Sci. USA 97, 6981\u20136985 (2000).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR5","doi-asserted-by":"publisher","first-page":"1301","DOI":"10.1126\/science.1134933","volume":"314","author":"P Roumagnac","year":"2006","unstructured":"Roumagnac, P. et al. Evolutionary history of Salmonella typhi. Science 314, 1301\u20131304 (2006).","journal-title":"Science"},{"key":"BFng3114_CR6","doi-asserted-by":"publisher","first-page":"15","DOI":"10.3389\/fmicb.2013.00015","volume":"4","author":"F Baquero","year":"2013","unstructured":"Baquero, F., Tedim, A.S. & Coque, T.M. Antibiotic resistance shaping multilevel population biology of bacteria. Front. Microbiol. 4, 15 (2013).","journal-title":"Front. Microbiol."},{"key":"BFng3114_CR7","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1056\/NEJMoa1012928","volume":"364","author":"CS Chin","year":"2011","unstructured":"Chin, C.S. et al. The origin of the Haitian cholera outbreak strain. N. Engl. J. Med. 364, 33\u201342 (2011).","journal-title":"N. Engl. J. Med."},{"key":"BFng3114_CR8","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1126\/science.1198545","volume":"331","author":"NJ Croucher","year":"2011","unstructured":"Croucher, N.J. et al. Rapid pneumococcal evolution in response to clinical interventions. Science 331, 430\u2013434 (2011).","journal-title":"Science"},{"key":"BFng3114_CR9","doi-asserted-by":"publisher","first-page":"730","DOI":"10.1056\/NEJMoa1003176","volume":"364","author":"JL Gardy","year":"2011","unstructured":"Gardy, J.L. et al. Whole-genome squencing and social-network analysis of a tuberculosis outbreak. N. Engl. J. Med. 364, 730\u2013739 (2011).","journal-title":"N. Engl. J. Med."},{"key":"BFng3114_CR10","doi-asserted-by":"publisher","first-page":"e22751","DOI":"10.1371\/journal.pone.0022751","volume":"6","author":"A Mellmann","year":"2011","unstructured":"Mellmann, A. et al. Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104: H4 outbreak by rapid next generation sequencing technology. PLoS ONE 6, e22751 (2011).","journal-title":"PLoS ONE"},{"key":"BFng3114_CR11","doi-asserted-by":"publisher","first-page":"2267","DOI":"10.1056\/NEJMoa1109910","volume":"366","author":"CU K\u00f6ser","year":"2012","unstructured":"K\u00f6ser, C.U. et al. Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N. Engl. J. Med. 366, 2267\u20132275 (2012).","journal-title":"N. Engl. J. Med."},{"key":"BFng3114_CR12","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1016\/S1473-3099(12)70268-2","volume":"13","author":"SR Harris","year":"2013","unstructured":"Harris, S.R. et al. Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect. Dis. 13, 130\u2013136 (2013).","journal-title":"Lancet Infect. Dis."},{"key":"BFng3114_CR13","doi-asserted-by":"publisher","first-page":"506","DOI":"10.1128\/CMR.15.3.506-526.2002","volume":"15","author":"BS Fields","year":"2002","unstructured":"Fields, B.S., Benson, R.F. & Besser, R.E. Legionella and Legionnaires' disease: 25 years of investigation. Clin. Microbiol. Rev. 15, 506\u2013526 (2002).","journal-title":"Clin. Microbiol. Rev."},{"key":"BFng3114_CR14","doi-asserted-by":"publisher","first-page":"1189","DOI":"10.1056\/NEJM197712012972201","volume":"297","author":"DW Fraser","year":"1977","unstructured":"Fraser, D.W. et al. Legionnaires' disease: description of an epidemic of pneumonia. N. Engl. J. Med. 297, 1189\u20131197 (1977).","journal-title":"N. Engl. J. Med."},{"key":"BFng3114_CR15","doi-asserted-by":"publisher","first-page":"729","DOI":"10.1007\/s10096-002-0819-9","volume":"21","author":"JA Fern\u00e1ndez","year":"2002","unstructured":"Fern\u00e1ndez, J.A., L\u00f3pez, P., Orozco, D. & Merino, J. Clinical study of an outbreak of Legionnaire's disease in Alcoy, Southeastern Spain. Eur. J. Clin. Microbiol. Infect. Dis. 21, 729\u2013735 (2002).","journal-title":"Eur. J. Clin. Microbiol. Infect. Dis."},{"key":"BFng3114_CR16","doi-asserted-by":"publisher","first-page":"1381","DOI":"10.3201\/eid1609.100248","volume":"16","author":"M Coscoll\u00e1","year":"2010","unstructured":"Coscoll\u00e1, M., Fenollar, J., Escribano, I. & Gonz\u00e1lez-Candelas, F. Legionellosis outbreak associated with asphalt paving machine, Spain, 2009. Emerg. Infect. Dis. 16, 1381\u20131387 (2010).","journal-title":"Emerg. Infect. Dis."},{"key":"BFng3114_CR17","doi-asserted-by":"publisher","first-page":"19982","DOI":"10.2807\/ese.16.40.19982-en","volume":"16","author":"M Rota","year":"2011","unstructured":"Rota, M. et al. Cluster of travel-associated Legionnaires' disease in Lazise, Italy, July to August 2011. Euro Surveill. 16, 19982 (2011).","journal-title":"Euro Surveill."},{"key":"BFng3114_CR18","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1093\/cid\/cit176","volume":"57","author":"PK Yiallouros","year":"2013","unstructured":"Yiallouros, P.K. et al. First outbreak of nosocomial Legionella infection in term neonates caused by a cold mist ultrasonic humidifier. Clin. Infect. Dis. 57, 48\u201356 (2013).","journal-title":"Clin. Infect. Dis."},{"key":"BFng3114_CR19","doi-asserted-by":"publisher","first-page":"19691","DOI":"10.2807\/ese.15.42.19691-en","volume":"15","author":"M Keramarou","year":"2010","unstructured":"Keramarou, M. & Evans, M.R. A community outbreak of Legionnaires' disease in South Wales, August\u2013September 2010. Euro Surveill. 15, 19691 (2010).","journal-title":"Euro Surveill."},{"key":"BFng3114_CR20","doi-asserted-by":"crossref","first-page":"20271","DOI":"10.2807\/ese.17.37.20271-en","volume":"17","author":"N Coetzee","year":"2012","unstructured":"Coetzee, N. et al. An outbreak of Legionnaires' disease associated with a display spa pool in retail premises, Stoke-on-Trent, United Kingdom, July 2012. Euro Surveill. 17, 20271 (2012).","journal-title":"Euro Surveill."},{"key":"BFng3114_CR21","doi-asserted-by":"publisher","first-page":"20216","DOI":"10.2807\/ese.17.28.20216-en","volume":"17","author":"D McCormick","year":"2012","unstructured":"McCormick, D. et al. Public health response to an outbreak of Legionnaires' disease in Edinburgh, United Kingdom, June 2012. Euro Surveill. 17, 20216 (2012).","journal-title":"Euro Surveill."},{"key":"BFng3114_CR22","doi-asserted-by":"publisher","first-page":"2932","DOI":"10.1128\/JCM.41.7.2932-2939.2003","volume":"41","author":"V Gaia","year":"2003","unstructured":"Gaia, V., Fry, N.K., Harrison, T.J. & Peduzzi, R. Sequence-based typing of Legionella pneumophila serogroup 1 offers the potential for true portability in legionellosis outbreak investigation. J. Clin. Microbiol. 41, 2932\u20132939 (2003).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3114_CR23","doi-asserted-by":"publisher","first-page":"2047","DOI":"10.1128\/JCM.43.5.2047-2052.2005","volume":"43","author":"V Gaia","year":"2005","unstructured":"Gaia, V. et al. Consensus sequence\u2013based scheme for epidemiological typing of clinical and environmental isolates of Legionella pneumophila. J. Clin. Microbiol. 43, 2047\u20132052 (2005).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3114_CR24","doi-asserted-by":"publisher","first-page":"1965","DOI":"10.1128\/JCM.00261-07","volume":"45","author":"S Ratzow","year":"2007","unstructured":"Ratzow, S., Gaia, V., Helbig, J.H., Fry, N.K. & Luck, P.C. Addition of neuA, the gene encoding N-acylneuraminate cytidylyl transferase, increases the discriminatory ability of the consensus sequence\u2013based scheme for typing Legionella pneumophila serogroup 1 strains. J. Clin. Microbiol. 45, 1965\u20131968 (2007).","journal-title":"J. Clin. Microbiol."},{"key":"BFng3114_CR25","doi-asserted-by":"publisher","first-page":"O435","DOI":"10.1111\/1469-0691.12459","volume":"20","author":"M Mentasti","year":"2014","unstructured":"Mentasti, M. et al. Extension of the Legionella pneumophila sequence-based typing scheme to include strains carrying a variant of the N-acylneuraminate cytidylyltransferase gene. Clin. Microbiol. Infect. 20, O435\u2013O441 (2014).","journal-title":"Clin. Microbiol. Infect."},{"key":"BFng3114_CR26","doi-asserted-by":"publisher","first-page":"985","DOI":"10.1093\/molbev\/msq278","volume":"28","author":"M Coscoll\u00e1","year":"2011","unstructured":"Coscoll\u00e1, M., Comas, I. & Gonz\u00e1lez-Candelas, F. Quantifying nonvertical inheritance in the evolution of Legionella pneumophila. Mol. Biol. Evol. 28, 985\u20131001 (2011).","journal-title":"Mol. Biol. Evol."},{"key":"BFng3114_CR27","doi-asserted-by":"publisher","first-page":"a009993","DOI":"10.1101\/cshperspect.a009993","volume":"3","author":"L Gomez-Valero","year":"2013","unstructured":"Gomez-Valero, L. & Buchrieser, C. Genome dynamics in legionella: the basis of versatility and adaptation to intracellular replication. Cold Spring Harb. Perspect. Med. 3, a009993 (2013).","journal-title":"Cold Spring Harb. Perspect. Med."},{"key":"BFng3114_CR28","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1186\/1471-2180-13-302","volume":"13","author":"AP Underwood","year":"2013","unstructured":"Underwood, A.P., Jones, G., Mentasti, M., Fry, N.K. & Harrison, T.G. Comparison of the Legionella pneumophila population structure as determined by sequence-based typing and whole genome sequencing. BMC Microbiol. 13, 302 (2013).","journal-title":"BMC Microbiol."},{"key":"BFng3114_CR29","doi-asserted-by":"publisher","first-page":"643","DOI":"10.1111\/j.1462-2920.2006.01184.x","volume":"9","author":"M Coscoll\u00e1","year":"2007","unstructured":"Coscoll\u00e1, M. & Gonz\u00e1lez-Candelas, F. Population structure and recombination in environmental isolates of Legionella pneumophila. Environ. Microbiol. 9, 643\u2013656 (2007).","journal-title":"Environ. Microbiol."},{"key":"BFng3114_CR30","doi-asserted-by":"publisher","first-page":"5027","DOI":"10.1073\/pnas.1016657108","volume":"108","author":"DA Rasko","year":"2011","unstructured":"Rasko, D.A. et al. Bacillus anthracis comparative genome analysis in support of the Amerithrax investigation. Proc. Natl. Acad. Sci. USA 108, 5027\u20135032 (2011).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR31","doi-asserted-by":"publisher","first-page":"e002175","DOI":"10.1136\/bmjopen-2012-002175","volume":"3","author":"S Reuter","year":"2013","unstructured":"Reuter, S. et al. A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak. BMJ Open 3, e002175 (2013).","journal-title":"BMJ Open"},{"key":"BFng3114_CR32","doi-asserted-by":"publisher","first-page":"305","DOI":"10.1038\/ng.2895","volume":"46","author":"C Chewapreecha","year":"2014","unstructured":"Chewapreecha, C. et al. Dense genomic sampling identifies highways of pneumococcal recombination. Nat. Genet. 46, 305\u2013309 (2014).","journal-title":"Nat. Genet."},{"key":"BFng3114_CR33","doi-asserted-by":"publisher","first-page":"656","DOI":"10.1038\/ng.2625","volume":"45","author":"NJ Croucher","year":"2013","unstructured":"Croucher, N.J. et al. Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat. Genet. 45, 656\u2013663 (2013).","journal-title":"Nat. Genet."},{"key":"BFng3114_CR34","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1038\/ng.2478","volume":"45","author":"M He","year":"2013","unstructured":"He, M. et al. Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat. Genet. 45, 109\u2013113 (2013).","journal-title":"Nat. Genet."},{"key":"BFng3114_CR35","doi-asserted-by":"publisher","first-page":"1056","DOI":"10.1038\/ng.2369","volume":"44","author":"KE Holt","year":"2012","unstructured":"Holt, K.E. et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat. Genet. 44, 1056\u20131059 (2012).","journal-title":"Nat. Genet."},{"key":"BFng3114_CR36","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1186\/1471-2164-11-181","volume":"11","author":"G D'Auria","year":"2010","unstructured":"D'Auria, G., Jimenez-Hernandez, N., Peris-Bondia, F., Moya, A. & Latorre, A. Legionella pneumophila pangenome reveals strain-specific virulence factors. BMC Genomics 11, 181 (2010).","journal-title":"BMC Genomics"},{"key":"BFng3114_CR37","doi-asserted-by":"publisher","first-page":"1551","DOI":"10.1016\/S0140-6736(13)60632-7","volume":"381","author":"JM Bryant","year":"2013","unstructured":"Bryant, J.M. et al. Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet 381, 1551\u20131560 (2013).","journal-title":"Lancet"},{"key":"BFng3114_CR38","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1016\/S1097-2765(00)80471-2","volume":"3","author":"C Bucci","year":"1999","unstructured":"Bucci, C. et al. Hypermutation in pathogenic bacteria: frequent phase variation in meningococci is a phenotypic trait of a specialized mutator biotype. Mol. Cell 3, 435\u2013445 (1999).","journal-title":"Mol. Cell"},{"key":"BFng3114_CR39","doi-asserted-by":"publisher","first-page":"13680","DOI":"10.1073\/pnas.1205357109","volume":"109","author":"MR Weigand","year":"2012","unstructured":"Weigand, M.R. & Sundin, G.W. General and inducible hypermutation facilitate parallel adaptation in Pseudomonas aeruginosa despite divergent mutation spectra. Proc. Natl. Acad. Sci. USA 109, 13680\u201313685 (2012).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR40","doi-asserted-by":"publisher","first-page":"1454","DOI":"10.1126\/science.1171908","volume":"324","author":"WP Hanage","year":"2009","unstructured":"Hanage, W.P., Fraser, C., Tang, J., Connor, T.R. & Corander, J. Hyper-recombination, diversity, and antibiotic resistance in Pneumococcus. Science 324, 1454\u20131457 (2009).","journal-title":"Science"},{"key":"BFng3114_CR41","doi-asserted-by":"publisher","first-page":"e56","DOI":"10.1371\/journal.pntd.0000056","volume":"1","author":"J Thaipadungpanit","year":"2007","unstructured":"Thaipadungpanit, J. et al. A dominant clone of Leptospira interrogans associated with an outbreak of human leptospirosis in Thailand. PLoS Negl. Trop. Dis. 1, e56 (2007).","journal-title":"PLoS Negl. Trop. Dis."},{"key":"BFng3114_CR42","doi-asserted-by":"publisher","first-page":"3702","DOI":"10.1128\/AEM.00244-08","volume":"74","author":"P Nicolas","year":"2008","unstructured":"Nicolas, P. et al. Population structure of the fish-pathogenic bacterium Flavobacterium psychrophilum. Appl. Environ. Microbiol. 74, 3702\u20133709 (2008).","journal-title":"Appl. Environ. Microbiol."},{"key":"BFng3114_CR43","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1038\/ismej.2008.93","volume":"3","author":"M Vos","year":"2009","unstructured":"Vos, M. & Didelot, X. A comparison of homologous recombination rates in bacteria and archaea. ISME J. 3, 199\u2013208 (2009).","journal-title":"ISME J."},{"key":"BFng3114_CR44","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1186\/1741-7007-3-6","volume":"3","author":"WP Hanage","year":"2005","unstructured":"Hanage, W.P., Fraser, C. & Spratt, B.G. Fuzzy species among recombinogenic bacteria. BMC Biol. 3, 6 (2005).","journal-title":"BMC Biol."},{"key":"BFng3114_CR45","doi-asserted-by":"publisher","first-page":"15961","DOI":"10.1073\/pnas.0803654105","volume":"105","author":"M Brochet","year":"2008","unstructured":"Brochet, M. et al. Shaping a bacterial genome by large chromosomal replacements, the evolutionary history of Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 105, 15961\u201315966 (2008).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR46","doi-asserted-by":"publisher","first-page":"7527","DOI":"10.1073\/pnas.0914322107","volume":"107","author":"M He","year":"2010","unstructured":"He, M. et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc. Natl. Acad. Sci. USA 107, 7527\u20137532 (2010).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR47","doi-asserted-by":"publisher","first-page":"e110","DOI":"10.1371\/journal.ppat.0030110","volume":"3","author":"K Velmurugan","year":"2007","unstructured":"Velmurugan, K. et al. Mycobacterium tuberculosis nuoG is a virulence gene that inhibits apoptosis of infected host cells. PLoS Pathog. 3, e110 (2007).","journal-title":"PLoS Pathog."},{"key":"BFng3114_CR48","doi-asserted-by":"publisher","first-page":"e1000864","DOI":"10.1371\/journal.ppat.1000864","volume":"6","author":"JL Miller","year":"2010","unstructured":"Miller, J.L., Velmurugan, K., Cowan, M.J. & Briken, V. The type I NADH dehydrogenase of Mycobacterium tuberculosis counters phagosomal NOX2 activity to inhibit TNF-\u03b1\u2013mediated host cell apoptosis. PLoS Pathog. 6, e1000864 (2010).","journal-title":"PLoS Pathog."},{"key":"BFng3114_CR49","doi-asserted-by":"publisher","first-page":"81","DOI":"10.1016\/j.chom.2011.11.012","volume":"11","author":"R Blomgran","year":"2012","unstructured":"Blomgran, R., Desvignes, L., Briken, V. & Ernst, J.D. Mycobacterium tuberculosis inhibits neutrophil apoptosis, leading to delayed activation of naive CD4 T cells. Cell Host Microbe 11, 81\u201390 (2012).","journal-title":"Cell Host Microbe"},{"key":"BFng3114_CR50","doi-asserted-by":"publisher","first-page":"744","DOI":"10.1101\/gr.086645.108","volume":"19","author":"WF Doolittle","year":"2009","unstructured":"Doolittle, W.F. & Zhaxybayeva, O. On the origin of prokaryotic species. Genome Res. 19, 744\u2013756 (2009).","journal-title":"Genome Res."},{"key":"BFng3114_CR51","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754\u20131760 (2009).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR52","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1101\/gr.074492.107","volume":"18","author":"DR Zerbino","year":"2008","unstructured":"Zerbino, D.R. & Birney, E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 18, 821\u2013829 (2008).","journal-title":"Genome Res."},{"key":"BFng3114_CR53","doi-asserted-by":"publisher","first-page":"421","DOI":"10.1186\/1471-2105-10-421","volume":"10","author":"C Camacho","year":"2009","unstructured":"Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).","journal-title":"BMC Bioinformatics"},{"key":"BFng3114_CR54","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li, H. et al. The Sequence Alignment\/Map format and SAMtools. Bioinformatics 25, 2078\u20132079 (2009).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR55","doi-asserted-by":"publisher","first-page":"11189","DOI":"10.1093\/nar\/gks918","volume":"40","author":"A Wilm","year":"2012","unstructured":"Wilm, A. et al. LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic Acids Res. 40, 11189\u201311201 (2012).","journal-title":"Nucleic Acids Res."},{"key":"BFng3114_CR56","doi-asserted-by":"publisher","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"ACE Darling","year":"2004","unstructured":"Darling, A.C.E., Mau, B., Blattner, F.R. & Perna, N.T. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 14, 1394\u20131403 (2004).","journal-title":"Genome Res."},{"key":"BFng3114_CR57","doi-asserted-by":"publisher","first-page":"e11147","DOI":"10.1371\/journal.pone.0011147","volume":"5","author":"AE Darling","year":"2010","unstructured":"Darling, A.E., Mau, B. & Perna, N.T. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS ONE 5, e11147 (2010).","journal-title":"PLoS ONE"},{"key":"BFng3114_CR58","doi-asserted-by":"publisher","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","volume":"25","author":"S Capella- Guti\u00e9rrez","year":"2009","unstructured":"Capella- Guti\u00e9rrez, S., Silla-Mart\u00ednez, J.M. & Gabald\u00f3n, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972\u20131973 (2009).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR59","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis, A. RAxML-VI-HPC: maximum likelihood\u2013based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22, 2688\u20132690 (2006).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR60","doi-asserted-by":"publisher","first-page":"2791","DOI":"10.1093\/bioinformatics\/bti403","volume":"21","author":"AJ Vilella","year":"2005","unstructured":"Vilella, A.J., Blanco-Garcia, A., Hutter, S. & Rozas, J. VariScan: analysis of evolutionary patterns from large-scale DNA sequence polymorphism data. Bioinformatics 21, 2791\u20132793 (2005).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR61","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1093\/molbev\/msr121","volume":"28","author":"K Tamura","year":"2011","unstructured":"Tamura, K. et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731\u20132739 (2011).","journal-title":"Mol. Biol. Evol."},{"key":"BFng3114_CR62","unstructured":"R Development Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, Vienna, 2011)."},{"key":"BFng3114_CR63","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1093\/bioinformatics\/btg412","volume":"20","author":"E Paradis","year":"2004","unstructured":"Paradis, E., Claude, J. & Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics 20, 289\u2013290 (2004).","journal-title":"Bioinformatics"},{"key":"BFng3114_CR64","doi-asserted-by":"publisher","first-page":"1969","DOI":"10.1093\/molbev\/mss075","volume":"29","author":"AJ Drummond","year":"2012","unstructured":"Drummond, A.J., Suchard, M.A., Xie, D. & Rambaut, A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969\u20131973 (2012).","journal-title":"Mol. Biol. Evol."},{"key":"BFng3114_CR65","doi-asserted-by":"publisher","first-page":"577","DOI":"10.1073\/pnas.1205750110","volume":"110","author":"Y Cui","year":"2013","unstructured":"Cui, Y. et al. Historical variations in mutation rate in an epidemic pathogen, Yersinia pestis. Proc. Natl. Acad. Sci. USA 110, 577\u2013582 (2013).","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"BFng3114_CR66","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1093\/bioinformatics\/18.3.502","volume":"18","author":"HA Schmidt","year":"2002","unstructured":"Schmidt, H.A., Strimmer, K., Vingron, M. & von Haeseler, A. TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18, 502\u2013504 (2002).","journal-title":"Bioinformatics"}],"container-title":["Nature Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.nature.com\/articles\/ng.3114.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ng.3114","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.nature.com\/articles\/ng.3114.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,18]],"date-time":"2023-05-18T21:02:24Z","timestamp":1684443744000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/ng.3114"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2014,10,5]]},"references-count":66,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2014,11]]}},"alternative-id":["BFng3114"],"URL":"https:\/\/doi.org\/10.1038\/ng.3114","relation":{},"ISSN":["1061-4036","1546-1718"],"issn-type":[{"value":"1061-4036","type":"print"},{"value":"1546-1718","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,10,5]]},"assertion":[{"value":"21 February 2014","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 September 2014","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 October 2014","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare no competing financial interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}