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(IDU)","volume":"43","author":"VR Nerurkar","year":"1997","journal-title":"Cell Mol Biol (Noisy-le-grand)"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/00042560-199701010-00001","article-title":"Genetic, antigenic and serologic characterization of human immunodeficiency virus type 1 from Indonesia","volume":"14","author":"KR Porter","year":"1997","journal-title":"J Acquir Immune Defic Syndr Hum Retrovirol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1089\/aid.2008.0095","article-title":"Identification of subtype B, multiple circulating recombinant forms and unique recombinants of HIV type 1 in an MSM cohort in China","volume":"24","author":"W Wang","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"136","DOI":"10.2174\/157016211795569096","article-title":"The dynamic face of HIV-1 subtypes among men who have sex with men in Beijing, 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Kihara","year":"1997","journal-title":"J Acquir Immune Defic Syndr Hum Retrovirol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1126\/science.1090727","article-title":"Unifying the epidemiological and evolutionary dynamics of pathogens","volume":"303","author":"BT Grenfell","year":"2004","journal-title":"Science"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1038\/nrg2053","article-title":"The evolution of epidemic influenza","volume":"8","author":"MI Nelson","year":"2007","journal-title":"Nat Rev Genet"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1371\/journal.ppat.0030131","article-title":"Phylogenetic analysis reveals the global migration of seasonal influenza A viruses","volume":"3","author":"MI Nelson","year":"2007","journal-title":"PLoS Pathog"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"e11057","DOI":"10.1371\/journal.pone.0011057","article-title":"Molecular evolutionary analysis of the influenza A(H1N1)pdm, May-September, 2009: temporal and spatial spreading profile of the viruses in Japan","volume":"5","author":"T Shiino","year":"2010","journal-title":"PLoS One"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"e1000198","DOI":"10.1371\/journal.pmed.1000198","article-title":"The global spread of hepatitis C virus 1a and 1b: a phylodynamic and phylogeographic analysis","volume":"6","author":"G Magiorkinis","year":"2009","journal-title":"PLoS Med"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1093\/molbev\/msg043","article-title":"The epidemiology and iatrogenic transmission of hepatitis C virus in Egypt: a Bayesian coalescent approach","volume":"20","author":"OG Pybus","year":"2003","journal-title":"Mol Biol Evol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e1000590","DOI":"10.1371\/journal.ppat.1000590","article-title":"Molecular phylodynamics of the heterosexual HIV epidemic in the United Kingdom","volume":"5","author":"GJ Hughes","year":"2009","journal-title":"PLoS Pathog"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1093\/infdis\/jir550","article-title":"Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic","volume":"204","author":"AJ Leigh Brown","year":"2011","journal-title":"J Infect Dis"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"e50","DOI":"10.1371\/journal.pmed.0050050","article-title":"Episodic sexual transmission of HIV revealed by molecular phylodynamics","volume":"5","author":"F Lewis","year":"2008","journal-title":"PLoS Med"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1016\/j.antiviral.2006.11.012","article-title":"Drug-resistant HIV-1 prevalence in patients newly diagnosed with HIV\/AIDS in Japan","volume":"75","author":"H Gatanaga","year":"2007","journal-title":"Antiviral Res"},{"key":"ref28","unstructured":"UNGASS (2012) National Commitments and Policies Instrument (NCPI). Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.unaids.org\/en\/dataanalysis\/knowyourresponse\/ncpi\/2012countries\/Japan\" xlink:type=\"simple\">http:\/\/www.unaids.org\/en\/dataanalysis\/knowyourresponse\/ncpi\/2012countries\/Japan<\/ext-link> NCPI 2012.pdf. Accessed 20 June 2012."},{"key":"ref29","doi-asserted-by":"crossref","first-page":"2947","DOI":"10.1093\/bioinformatics\/btm404","article-title":"Clustal W and Clustal X version 2.0","volume":"23","author":"MA Larkin","year":"2007","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1316","DOI":"10.1126\/science.1061076","article-title":"Epidemiology. How viruses spread among computers and people","volume":"292","author":"AL Lloyd","year":"2001","journal-title":"Science"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e11170","DOI":"10.1371\/journal.pone.0011170","article-title":"Social networks shape the transmission dynamics of hepatitis C virus","volume":"5","author":"CM Romano","year":"2010","journal-title":"PLoS One"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"509","DOI":"10.1126\/science.286.5439.509","article-title":"Emergence of scaling in random networks","volume":"286","author":"AL Barabasi","year":"1999","journal-title":"Science"},{"key":"ref33","unstructured":"R Development Core Team (2010) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing. Available: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.r-project.org\/\" xlink:type=\"simple\">http:\/\/www.r-project.org\/<\/ext-link>."},{"key":"ref34","doi-asserted-by":"crossref","first-page":"11030","DOI":"10.1073\/pnas.0404206101","article-title":"Prospects for inferring very large phylogenies by using the neighbor-joining method","volume":"101","author":"K Tamura","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"2731","DOI":"10.1093\/molbev\/msr121","article-title":"MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods","volume":"28","author":"K Tamura","year":"2011","journal-title":"Mol Biol Evol"},{"key":"ref36","unstructured":"Swofford DL (2003) PAUP. Phylogenetic Analysis Using Parsimony (and Other Methods). Version 4. Sunderland, Massachusetts: Sinauer Associates."},{"key":"ref37","unstructured":"Nylander JAA (2004) MrModeltest v2. Program distributed by the author. Uppsala University: Evolutionary Biology Centre."},{"key":"ref38","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1186\/1471-2148-7-214","article-title":"BEAST: Bayesian evolutionary analysis by sampling trees","volume":"7","author":"AJ Drummond","year":"2007","journal-title":"BMC Evol Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1093\/oxfordjournals.molbev.a003872","article-title":"Bayesian selection of continuous-time Markov chain evolutionary models","volume":"18","author":"MA Suchard","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate model selection of relaxed molecular clocks in bayesian phylogenetics","volume":"30","author":"G Baele","year":"2013","journal-title":"Mol Biol Evol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"150","DOI":"10.1093\/sysbio\/syq085","article-title":"Improving marginal likelihood estimation for Bayesian phylogenetic model selection","volume":"60","author":"W Xie","year":"2011","journal-title":"Syst Biol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1038\/ncomms1325","article-title":"A novel methodology for large-scale phylogeny partition","volume":"2","author":"MC Prosperi","year":"2011","journal-title":"Nat Commun"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1093\/oxfordjournals.molbev.a003920","article-title":"The inference of stepwise changes in substitution rates using serial sequence samples","volume":"18","author":"A Drummond","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"1807","DOI":"10.1093\/oxfordjournals.molbev.a026281","article-title":"Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA","volume":"17","author":"A Drummond","year":"2000","journal-title":"Mol Biol 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