{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,24]],"date-time":"2025-09-24T10:21:26Z","timestamp":1758709286247},"reference-count":47,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2012,12,1]],"date-time":"2012-12-01T00:00:00Z","timestamp":1354320000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Retrovirology"],"published-print":{"date-parts":[[2012,12]]},"DOI":"10.1186\/1742-4690-9-108","type":"journal-article","created":{"date-parts":[[2012,12,17]],"date-time":"2012-12-17T19:14:04Z","timestamp":1355771644000},"source":"Crossref","is-referenced-by-count":24,"title":["High-resolution deep sequencing reveals biodiversity, population structure, and persistence of HIV-1 quasispecies within host ecosystems"],"prefix":"10.1186","volume":"9","author":[{"given":"Li","family":"Yin","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Li","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yijun","family":"Sun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wei","family":"Hou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanda C","family":"Lowe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brent P","family":"Gardner","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marco","family":"Salemi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wilton B","family":"Williams","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"William G","family":"Farmerie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John W","family":"Sleasman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maureen M","family":"Goodenow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,12,17]]},"reference":[{"issue":"2","key":"3377_CR1","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1016\/j.virusres.2007.07.001","volume":"129","author":"J Garcia-Arriaza","year":"2007","unstructured":"Garcia-Arriaza J, Domingo E, Briones C: Characterization of minority subpopulations in the mutant spectrum of HIV-1 quasispecies by successive specific amplifications. Virus Res. 2007, 129 (2): 123-134. 10.1016\/j.virusres.2007.07.001.","journal-title":"Virus Res"},{"issue":"1","key":"3377_CR2","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1016\/j.antiviral.2009.09.015","volume":"85","author":"R Paredes","year":"2010","unstructured":"Paredes R, Clotet B: Clinical management of HIV-1 resistance. Antiviral Res. 2010, 85 (1): 245-265. 10.1016\/j.antiviral.2009.09.015.","journal-title":"Antiviral Res"},{"issue":"Suppl 2","key":"3377_CR3","doi-asserted-by":"publisher","first-page":"S309","DOI":"10.1086\/655653","volume":"202","author":"CL Boutwell","year":"2010","unstructured":"Boutwell CL, Rolland MM, Herbeck JT, Mullins JI, Allen TM: Viral evolution and escape during acute HIV-1 infection. J Infect Dis. 2010, 202 (Suppl 2): S309-314.","journal-title":"J Infect Dis"},{"issue":"4","key":"3377_CR4","first-page":"344","volume":"2","author":"M Goodenow","year":"1989","unstructured":"Goodenow M, Huet T, Saurin W, Kwok S, Sninsky J, Wain-Hobson S: HIV-1 isolates are rapidly evolving quasispecies: evidence for viral mixtures and preferred nucleotide substitutions. J Acquir Immune Defic Syndr. 1989, 2 (4): 344-352.","journal-title":"J Acquir Immune Defic Syndr"},{"issue":"7","key":"3377_CR5","doi-asserted-by":"crossref","first-page":"3951","DOI":"10.1128\/JVI.67.7.3951-3960.1993","volume":"67","author":"SL Lamers","year":"1993","unstructured":"Lamers SL, Sleasman JW, She JX, Barrie KA, Pomeroy SM, Barrett DJ, Goodenow MM: Independent variation and positive selection in env V1 and V2 domains within maternal-infant strains of human immunodeficiency virus type 1 in vivo. J Virol. 1993, 67 (7): 3951-3960.","journal-title":"J Virol"},{"issue":"1","key":"3377_CR6","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1172\/JCI116970","volume":"93","author":"SL Lamers","year":"1994","unstructured":"Lamers SL, Sleasman JW, She JX, Barrie KA, Pomeroy SM, Barrett DJ, Goodenow MM: Persistence of multiple maternal genotypes of human immunodeficiency virus type I in infants infected by vertical transmission. J Clin Invest. 1994, 93 (1): 380-390. 10.1172\/JCI116970.","journal-title":"J Clin Invest"},{"issue":"4","key":"3377_CR7","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1016\/S1369-5274(03)00096-1","volume":"6","author":"DC Nickle","year":"2003","unstructured":"Nickle DC, Shriner D, Mittler JE, Frenkel LM, Mullins JI: Importance and detection of virus reservoirs and compartments of HIV infection. Curr Opin Microbiol. 2003, 6 (4): 410-416. 10.1016\/S1369-5274(03)00096-1.","journal-title":"Curr Opin Microbiol"},{"issue":"11","key":"3377_CR8","doi-asserted-by":"publisher","first-page":"1095","DOI":"10.1097\/00002030-199011000-00007","volume":"4","author":"MA Nowak","year":"1990","unstructured":"Nowak MA, May RM, Anderson RM: The evolutionary dynamics of HIV-1 quasispecies and the development of immunodeficiency disease. AIDS. 1990, 4 (11): 1095-1103. 10.1097\/00002030-199011000-00007.","journal-title":"AIDS"},{"issue":"9","key":"3377_CR9","doi-asserted-by":"publisher","first-page":"e950","DOI":"10.1371\/journal.pone.0000950","volume":"2","author":"M Salemi","year":"2007","unstructured":"Salemi M, Burkhardt BR, Gray RR, Ghaffari G, Sleasman JW, Goodenow MM: Phylodynamics of HIV-1 in lymphoid and non-lymphoid tissues reveals a central role for the thymus in emergence of CXCR4-using quasispecies. PLoS One. 2007, 2 (9): e950-10.1371\/journal.pone.0000950.","journal-title":"PLoS One"},{"issue":"12","key":"3377_CR10","doi-asserted-by":"crossref","first-page":"5840","DOI":"10.1128\/JVI.64.12.5840-5850.1990","volume":"64","author":"P Simmonds","year":"1990","unstructured":"Simmonds P, Balfe P, Ludlam CA, Bishop JO, Brown AJ: Analysis of sequence diversity in hypervariable regions of the external glycoprotein of human immunodeficiency virus type 1. J Virol. 1990, 64 (12): 5840-5850.","journal-title":"J Virol"},{"issue":"5048","key":"3377_CR11","doi-asserted-by":"publisher","first-page":"1134","DOI":"10.1126\/science.1546316","volume":"255","author":"SM Wolinsky","year":"1992","unstructured":"Wolinsky SM, Wike CM, Korber BT, Hutto C, Parks WP, Rosenblum LL, Kunstman KJ, Furtado MR, Munoz JL: Selective transmission of human immunodeficiency virus type-1 variants from mothers to infants. Science. 1992, 255 (5048): 1134-1137. 10.1126\/science.1546316.","journal-title":"Science"},{"issue":"5","key":"3377_CR12","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1086\/596736","volume":"199","author":"BB Simen","year":"2009","unstructured":"Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD, Huang C, Lubeski C, Turenchalk GS, Braverman MS, Desany B, Rothberg JM, Egholm M, Kozal MJ: Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis. 2009, 199 (5): 693-701. 10.1086\/596736.","journal-title":"J Infect Dis"},{"issue":"5","key":"3377_CR13","doi-asserted-by":"publisher","first-page":"e5683","DOI":"10.1371\/journal.pone.0005683","volume":"4","author":"AM Tsibris","year":"2009","unstructured":"Tsibris AM, Korber B, Arnaout R, Russ C, Lo CC, Leitner T, Gaschen B, Theiler J, Paredes R, Su Z, Hughes MD, Gulick RM, Greaves W, Coakley E, Flexner C, Nusbaum C, Kuritzkes DR: Quantitative deep sequencing reveals dynamic HIV-1 escape and large population shifts during CCR5 antagonist therapy in vivo. PLoS One. 2009, 4 (5): e5683-10.1371\/journal.pone.0005683.","journal-title":"PLoS One"},{"issue":"3","key":"3377_CR14","doi-asserted-by":"publisher","first-page":"e1002529","DOI":"10.1371\/journal.ppat.1002529","volume":"8","author":"MR Henn","year":"2012","unstructured":"Henn MR, Boutwell CL, Charlebois P, Lennon NJ, Power KA, Macalalad AR, Berlin AM, Malboeuf CM, Ryan EM, Gnerre S, Zody MC, Erlich RL, Green LM, Berical A, Wang Y, Casali M, Streeck H, Bloom AK, Dudek T, Tully D, Newman R, Axten KL, Gladden AD, Battis L, Kemper M, Zeng Q, Shea TP, Gujja S, Zedlack C, Gasser O, Brander C, Hess C, Gunthard HF, Brumme ZL, Brumme CJ, Bazner S, Rychert J, Tinsley JP, Mayer KH, Rosenberg E, Pereyra F, Levin JZ, Young SK, Jessen H, Altfeld M, Birren BW, Walker BD, Allen TM: Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 2012, 8 (3): e1002529-10.1371\/journal.ppat.1002529.","journal-title":"PLoS Pathog"},{"issue":"4","key":"3377_CR15","doi-asserted-by":"publisher","first-page":"819","DOI":"10.1093\/molbev\/msp289","volume":"27","author":"AF Poon","year":"2009","unstructured":"Poon AF, Swenson LC, Dong WW, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SD: Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol. 2009, 27 (4): 819-832.","journal-title":"Mol Biol Evol"},{"issue":"4","key":"3377_CR16","doi-asserted-by":"publisher","first-page":"e1000074","DOI":"10.1371\/journal.pcbi.1000074","volume":"4","author":"N Eriksson","year":"2008","unstructured":"Eriksson N, Pachter L, Mitsuya Y, Rhee SY, Wang C, Gharizadeh B, Ronaghi M, Shafer RW, Beerenwinkel N: Viral population estimation using pyrosequencing. PLoS Comput Biol. 2008, 4 (4): e1000074-","journal-title":"PLoS Comput Biol"},{"issue":"16","key":"3377_CR17","doi-asserted-by":"publisher","first-page":"8247","DOI":"10.1128\/JVI.00897-09","volume":"83","author":"BN Bimber","year":"2009","unstructured":"Bimber BN, Burwitz BJ, O\u2019Connor S, Detmer A, Gostick E, Lank SM, Price DA, Hughes A, O\u2019Connor D: Ultradeep pyrosequencing detects complex patterns of CD8+ T-lymphocyte escape in simian immunodeficiency virus-infected macaques. J Virol. 2009, 83 (16): 8247-8253. 10.1128\/JVI.00897-09.","journal-title":"J Virol"},{"issue":"12","key":"3377_CR18","doi-asserted-by":"publisher","first-page":"12ra23","DOI":"10.1126\/scitranslmed.3000540","volume":"1","author":"SD Boyd","year":"2009","unstructured":"Boyd SD, Marshall EL, Merker JD, Maniar JM, Zhang LN, Sahaf B, Jones CD, Simen BB, Hanczaruk B, Nguyen KD, Nadeau KC, Egholm M, Miklos DB, Zehnder JL, Fire AZ: Measurement and clinical monitoring of human lymphocyte clonality by massively parallel VDJ pyrosequencing. Sci Transl Med. 2009, 1 (12): 12ra23-10.1126\/scitranslmed.3000540.","journal-title":"Sci Transl Med"},{"issue":"3","key":"3377_CR19","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1016\/j.chom.2009.08.003","volume":"6","author":"AL Goodman","year":"2009","unstructured":"Goodman AL, McNulty NP, Zhao Y, Leip D, Mitra RD, Lozupone CA, Knight R, Gordon JI: Identifying genetic determinants needed to establish a human gut symbiont in its habitat. Cell Host Microbe. 2009, 6 (3): 279-289. 10.1016\/j.chom.2009.08.003.","journal-title":"Cell Host Microbe"},{"issue":"7","key":"3377_CR20","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.1101\/gr.085464.108","volume":"19","author":"M Hamady","year":"2009","unstructured":"Hamady M, Knight R: Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Res. 2009, 19 (7): 1141-1152. 10.1101\/gr.085464.108.","journal-title":"Genome Res"},{"issue":"11","key":"3377_CR21","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1177\/154405910808701104","volume":"87","author":"BJ Keijser","year":"2008","unstructured":"Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, Montijn RC, ten Cate JM, Crielaard W: Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res. 2008, 87 (11): 1016-1020. 10.1177\/154405910808701104.","journal-title":"J Dent Res"},{"issue":"4","key":"3377_CR22","doi-asserted-by":"crossref","first-page":"1721","DOI":"10.1128\/AEM.65.4.1721-1730.1999","volume":"65","author":"AE McCaig","year":"1999","unstructured":"McCaig AE, Glover LA, Prosser JI: Molecular analysis of bacterial community structure and diversity in unimproved and improved upland grass pastures. Appl Environ Microbiol. 1999, 65 (4): 1721-1730.","journal-title":"Appl Environ Microbiol"},{"issue":"3","key":"3377_CR23","doi-asserted-by":"publisher","first-page":"1501","DOI":"10.1128\/AEM.71.3.1501-1506.2005","volume":"71","author":"PD Schloss","year":"2005","unstructured":"Schloss PD, Handelsman J: Introducing DOTUR, a computer program for defining operational taxonomic units and estimating species richness. Appl Environ Microbiol. 2005, 71 (3): 1501-1506. 10.1128\/AEM.71.3.1501-1506.2005.","journal-title":"Appl Environ Microbiol"},{"issue":"32","key":"3377_CR24","doi-asserted-by":"publisher","first-page":"12115","DOI":"10.1073\/pnas.0605127103","volume":"103","author":"ML Sogin","year":"2006","unstructured":"Sogin ML, Morrison HG, Huber JA, Mark WD, Huse SM, Neal PR, Arrieta JM, Herndl GJ: Microbial diversity in the deep sea and the underexplored \u201crare biosphere\u201d. Proc Natl Acad Sci U S A. 2006, 103 (32): 12115-12120. 10.1073\/pnas.0605127103.","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"10","key":"3377_CR25","doi-asserted-by":"publisher","first-page":"e76","DOI":"10.1093\/nar\/gkp285","volume":"37","author":"Y Sun","year":"2009","unstructured":"Sun Y, Cai Y, Liu L, Yu F, Farrell ML, McKendree W, Farmerie W: ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences. Nucleic Acids Res. 2009, 37 (10): e76-10.1093\/nar\/gkp285.","journal-title":"Nucleic Acids Res"},{"issue":"5928","key":"3377_CR26","doi-asserted-by":"publisher","first-page":"807","DOI":"10.1126\/science.1170020","volume":"324","author":"JA Weinstein","year":"2009","unstructured":"Weinstein JA, Jiang N, White RA, Fisher DS, Quake SR: High-throughput sequencing of the zebrafish antibody repertoire. Science. 2009, 324 (5928): 807-810. 10.1126\/science.1170020.","journal-title":"Science"},{"issue":"2","key":"3377_CR27","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1046\/j.1365-2664.2003.00803.x","volume":"40","author":"A Campbell","year":"2003","unstructured":"Campbell A: Save those molecules: molecular biodiversity and life. Journal of Applied Ecology. 2003, 40 (2): 193-203. 10.1046\/j.1365-2664.2003.00803.x.","journal-title":"Journal of Applied Ecology"},{"key":"3377_CR28","volume-title":"Forest Ecology and preservation: A Handbook of Techniques","author":"AC Newton","year":"1999","unstructured":"Newton AC: Forest Ecology and preservation: A Handbook of Techniques. 1999, Oxford: Illustarted Edition edition"},{"issue":"7402","key":"3377_CR29","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"Human Microbiome Project Consortium","year":"2012","unstructured":"Human Microbiome Project Consortium: Structure, function and diversity of the healthy human microbiome. Nature. 2012, 486 (7402): 207-214. 10.1038\/nature11234.","journal-title":"Nature"},{"issue":"13","key":"3377_CR30","doi-asserted-by":"publisher","first-page":"1631","DOI":"10.1097\/QAD.0b013e32832e0599","volume":"23","author":"SK Ho","year":"2009","unstructured":"Ho SK, Perez EE, Rose SL, Coman RM, Lowe AC, Hou W, Ma C, Lawrence RM, Dunn BM, Sleasman JW, Goodenow MM: Genetic determinants in HIV-1 Gag and Env V3 are related to viral response to combination antiretroviral therapy with a protease inhibitor. AIDS. 2009, 23 (13): 1631-1640. 10.1097\/QAD.0b013e32832e0599.","journal-title":"AIDS"},{"key":"3377_CR31","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/1742-4690-6-15","volume":"6","author":"G Rozera","year":"2009","unstructured":"Rozera G, Abbate I, Bruselles A, Vlassi C, D\u2019Offizi G, Narciso P, Chillemi G, Prosperi M, Ippolito G, Capobianchi MR: Massively parallel pyrosequencing highlights minority variants in the HIV-1 env quasispecies deriving from lymphomonocyte sub-populations. Retrovirology. 2009, 6: 15-10.1186\/1742-4690-6-15.","journal-title":"Retrovirology"},{"key":"3377_CR32","doi-asserted-by":"publisher","first-page":"151","DOI":"10.1146\/annurev.micro.51.1.151","volume":"51","author":"E Domingo","year":"1997","unstructured":"Domingo E, Holland JJ: RNA virus mutations and fitness for survival. Annu Rev Microbiol. 1997, 51: 151-178. 10.1146\/annurev.micro.51.1.151.","journal-title":"Annu Rev Microbiol"},{"issue":"6","key":"3377_CR33","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1016\/0966-842X(96)20011-3","volume":"4","author":"M Eigen","year":"1996","unstructured":"Eigen M: On the nature of virus quasispecies. Trends Microbiol. 1996, 4 (6): 216-218. 10.1016\/0966-842X(96)20011-3.","journal-title":"Trends Microbiol"},{"issue":"7","key":"3377_CR34","doi-asserted-by":"publisher","first-page":"e1001005","DOI":"10.1371\/journal.ppat.1001005","volume":"6","author":"AS Lauring","year":"2010","unstructured":"Lauring AS, Andino R: Quasispecies theory and the behavior of RNA viruses. PLoS Pathog. 2010, 6 (7): e1001005-10.1371\/journal.ppat.1001005.","journal-title":"PLoS Pathog"},{"issue":"3","key":"3377_CR35","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1097\/00002030-199803000-00007","volume":"12","author":"FJ Paladin","year":"1998","unstructured":"Paladin FJ, Monzon OT, Tsuchie H, Aplasca MR, Learn GH, Kurimura T: Genetic subtypes of HIV-1 in the Philippines. AIDS. 1998, 12 (3): 291-300. 10.1097\/00002030-199803000-00007.","journal-title":"AIDS"},{"key":"3377_CR36","unstructured":"Los Alamos data base. 2012, http:\/\/www.hiv.lanl.gov\/content\/index ."},{"issue":"9","key":"3377_CR37","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.1093\/infdis\/jis503","volume":"206","author":"AD Redd","year":"2012","unstructured":"Redd AD, Collinson-Streng AN, Chatziandreou N, Mullis CE, Laeyendecker O, Martens C, Ricklefs S, Kiwanuka N, Nyein PH, Lutalo T, Grabowski MK, Kong X, Manucci J, Sewankambo N, Wawer MJ, Gray RH, Porcella SF, Fauci AS, Sagar M, Serwadda D, Quinn TC: Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions. J Infect Dis. 2012, 206 (9): 1433-1442. 10.1093\/infdis\/jis503.","journal-title":"J Infect Dis"},{"issue":"21","key":"3377_CR38","doi-asserted-by":"publisher","first-page":"11477","DOI":"10.1128\/JVI.78.21.11477-11486.2004","volume":"78","author":"CR Coberley","year":"2004","unstructured":"Coberley CR, Kohler JJ, Brown JN, Oshier JT, Baker HV, Popp MP, Sleasman JW, Goodenow MM: Impact on genetic networks in human macrophages by a CCR5 strain of human immunodeficiency virus type 1. J Virol. 2004, 78 (21): 11477-11486. 10.1128\/JVI.78.21.11477-11486.2004.","journal-title":"J Virol"},{"issue":"21","key":"3377_CR39","doi-asserted-by":"publisher","first-page":"13250","DOI":"10.1128\/JVI.79.21.13250-13261.2005","volume":"79","author":"G Ghaffari","year":"2005","unstructured":"Ghaffari G, Tuttle DL, Briggs D, Burkhardt BR, Bhatt D, Andiman WA, Sleasman JW, Goodenow MM: Complex determinants in human immunodeficiency virus type 1 envelope gp120 mediate CXCR4-dependent infection of macrophages. J Virol. 2005, 79 (21): 13250-13261. 10.1128\/JVI.79.21.13250-13261.2005.","journal-title":"J Virol"},{"issue":"3","key":"3377_CR40","doi-asserted-by":"publisher","first-page":"502","DOI":"10.1093\/bioinformatics\/18.3.502","volume":"18","author":"HA Schmidt","year":"2002","unstructured":"Schmidt HA, Strimmer K, Vingron M, von HA: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics. 2002, 18 (3): 502-504. 10.1093\/bioinformatics\/18.3.502.","journal-title":"Bioinformatics"},{"key":"3377_CR41","doi-asserted-by":"publisher","first-page":"6815","DOI":"10.1073\/pnas.94.13.6815","volume":"94","author":"K Strimmer","year":"1997","unstructured":"Strimmer K, von Haeseler A: Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A. 1997, 94: 6815-6819. 10.1073\/pnas.94.13.6815.","journal-title":"Proc Natl Acad Sci U S A"},{"key":"3377_CR42","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/S1055-7903(02)00326-3","volume":"26","author":"X Xia","year":"2003","unstructured":"Xia X, Xie Z, Salemi M, Chen L, Wang Y: An index of substitution saturation and its application. Mol Phylogenet Evol. 2003, 26: 1-7. 10.1016\/S1055-7903(02)00326-3.","journal-title":"Mol Phylogenet Evol"},{"issue":"3","key":"3377_CR43","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1093\/sysbio\/syq010","volume":"59","author":"S Guindon","year":"2010","unstructured":"Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O: New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010, 59 (3): 307-321. 10.1093\/sysbio\/syq010.","journal-title":"Syst Biol"},{"key":"3377_CR44","first-page":"160","volume-title":"The Phylogenetic Handbook-a Practical Approach to DNA and Protein Phylogeny","author":"DSJ Swofford","year":"2003","unstructured":"Swofford DSJ: Phylogeny inference based on parsimony and other methods with PAUP*. The Phylogenetic Handbook-a Practical Approach to DNA and Protein Phylogeny. Edited by: Lemey P, Salemi M, Vandamme A-M. 2003, New York: Cambrige University Press, 160-206. 2","edition":"2"},{"issue":"1","key":"3377_CR45","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.ympev.2010.01.019","volume":"56","author":"RR Gray","year":"2010","unstructured":"Gray RR, Veras NM, Santos LA, Salemi M: Evolutionary characterization of the West Nile Virus complete genome. Mol Phylogenet Evol. 2010, 56 (1): 195-200. 10.1016\/j.ympev.2010.01.019.","journal-title":"Mol Phylogenet Evol"},{"issue":"Pt 7","key":"3377_CR46","doi-asserted-by":"publisher","first-page":"1698","DOI":"10.1099\/vir.0.028951-0","volume":"92","author":"NM Veras","year":"2011","unstructured":"Veras NM, Gray RR, Brigido LF, Rodrigues R, Salemi M: High-resolution phylogenetics and phylogeography of human immunodeficiency virus type 1 subtype C epidemic in South America. J Gen Virol. 2011, 92 (Pt 7): 1698-1709.","journal-title":"J Gen Virol"},{"issue":"5","key":"3377_CR47","first-page":"555","volume":"13","author":"Z Yang","year":"1997","unstructured":"Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci. 1997, 13 (5): 555-556.","journal-title":"Comput Appl Biosci"}],"container-title":["Retrovirology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1742-4690-9-108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1742-4690-9-108\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1742-4690-9-108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,7,18]],"date-time":"2020-07-18T22:03:34Z","timestamp":1595109814000},"score":1,"resource":{"primary":{"URL":"https:\/\/retrovirology.biomedcentral.com\/articles\/10.1186\/1742-4690-9-108"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,12]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2012,12]]}},"alternative-id":["3377"],"URL":"https:\/\/doi.org\/10.1186\/1742-4690-9-108","relation":{},"ISSN":["1742-4690"],"issn-type":[{"value":"1742-4690","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,12]]},"article-number":"108"}}