{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,8,26]],"date-time":"2023-08-26T10:51:42Z","timestamp":1693047102247},"reference-count":55,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2011,3,8]],"date-time":"2011-03-08T00:00:00Z","timestamp":1299542400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Evol Biol"],"published-print":{"date-parts":[[2011,12]]},"DOI":"10.1186\/1471-2148-11-62","type":"journal-article","created":{"date-parts":[[2011,3,9]],"date-time":"2011-03-09T07:42:59Z","timestamp":1299656579000},"source":"Crossref","is-referenced-by-count":9,"title":["HIV-1 infected monozygotic twins: a tale of two outcomes"],"prefix":"10.1186","volume":"11","author":[{"given":"Loubna","family":"Tazi","sequence":"first","affiliation":[]},{"given":"Hiromi","family":"Imamichi","sequence":"additional","affiliation":[]},{"given":"Steven","family":"Hirschfeld","sequence":"additional","affiliation":[]},{"given":"Julia A","family":"Metcalf","sequence":"additional","affiliation":[]},{"given":"Susan","family":"Orsega","sequence":"additional","affiliation":[]},{"given":"Marcos","family":"P\u00e9rez-Losada","sequence":"additional","affiliation":[]},{"given":"David","family":"Posada","sequence":"additional","affiliation":[]},{"given":"H Clifford","family":"Lane","sequence":"additional","affiliation":[]},{"given":"Keith A","family":"Crandall","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,3,8]]},"reference":[{"key":"1678_CR1","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1590\/S0074-02761998000500002","volume":"93","author":"PW Ewald","year":"1998","unstructured":"Ewald PW, Sussman JB, Distler MT, Libel C, Chammas WP, Dirita VJ, Salles CA, Vicente AC, Heitmann I, Cabello F: Evolutionary control of infectious disease: prospects for vectorborne and waterborne pathogens. Mem Inst Oswaldo Cruz. 1998, 93: 567-576. 10.1590\/S0074-02761998000500002.","journal-title":"Mem Inst Oswaldo Cruz"},{"key":"1678_CR2","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1023\/A:1009999502884","volume":"3","author":"A Gammelgaard","year":"2000","unstructured":"Gammelgaard A: Evolutionary biology and the concept of disease. Med Health Care Philos. 2000, 3: 109-116. 10.1023\/A:1009999502884.","journal-title":"Med Health Care Philos"},{"key":"1678_CR3","doi-asserted-by":"publisher","first-page":"1207","DOI":"10.1126\/science.1179152","volume":"325","author":"PT Ellison","year":"2009","unstructured":"Ellison PT: Evolutionary biology for doctors. Science. 2009, 325: 1207-10.1126\/science.1179152.","journal-title":"Science"},{"key":"1678_CR4","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1111\/j.1420-9101.2007.01480.x","volume":"21","author":"SA Frank","year":"2008","unstructured":"Frank SA, Schmid-Hempel P: Mechanisms of pathogenesis and the evolution of parasite virulence. J Evol Biol. 2008, 21: 396-404. 10.1111\/j.1420-9101.2007.01480.x.","journal-title":"J Evol Biol"},{"key":"1678_CR5","first-page":"143","volume":"176","author":"JM Coffin","year":"1992","unstructured":"Coffin JM: Genetic diversity and evolution of retroviruses. Curr Top Microbiol Immunol. 1992, 176: 143-164.","journal-title":"Curr Top Microbiol Immunol"},{"key":"1678_CR6","doi-asserted-by":"publisher","first-page":"117","DOI":"10.1038\/373117a0","volume":"373","author":"X Wei","year":"1995","unstructured":"Wei X, Ghosh SK, Taylor ME, Johnson VA, Emini EA, Deutsch P, Lifson JD, Bonhoeffer S, Nowak MA, Hahn BH, et al: Viral dynamics in human immunodeficiency virus type 1 infection. Nature. 1995, 373: 117-122. 10.1038\/373117a0.","journal-title":"Nature"},{"key":"1678_CR7","doi-asserted-by":"publisher","first-page":"630","DOI":"10.1038\/nri1417","volume":"4","author":"PJ Goulder","year":"2004","unstructured":"Goulder PJ, Watkins DI: HIV and SIV CTL escape: implications for vaccine design. Nat Rev Immunol. 2004, 4: 630-640. 10.1038\/nri1417.","journal-title":"Nat Rev Immunol"},{"key":"1678_CR8","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1126\/science.1161000","volume":"321","author":"AS Fauci","year":"2008","unstructured":"Fauci AS, Johnston MI, Dieffenbach CW, Burton DR, Hammer SM, Hoxie JA, Martin M, Overbaugh J, Watkins DI, Mahmoud A, et al: HIV vaccine research: the way forward. Science. 2008, 321: 530-532. 10.1126\/science.1161000.","journal-title":"Science"},{"key":"1678_CR9","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1146\/annurev.micro.50.1.825","volume":"50","author":"G Pantaleo","year":"1996","unstructured":"Pantaleo G, Fauci AS: Immunopathogenesis of HIV infection. Annu Rev Microbiol. 1996, 50: 825-854. 10.1146\/annurev.micro.50.1.825.","journal-title":"Annu Rev Microbiol"},{"key":"1678_CR10","doi-asserted-by":"publisher","first-page":"861","DOI":"10.1038\/nm0703-861","volume":"9","author":"NL Letvin","year":"2003","unstructured":"Letvin NL, Walker BD: Immunopathogenesis and immunotherapy in AIDS virus infections. Nat Med. 2003, 9: 861-866. 10.1038\/nm0703-861.","journal-title":"Nat Med"},{"key":"1678_CR11","doi-asserted-by":"publisher","first-page":"1439","DOI":"10.1126\/science.1069660","volume":"296","author":"CB Moore","year":"2002","unstructured":"Moore CB, John M, James IR, Christiansen FT, Witt CS, Mallal SA: Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science. 2002, 296: 1439-1443. 10.1126\/science.1069660.","journal-title":"Science"},{"key":"1678_CR12","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1084\/jem.20022138","volume":"197","author":"OO Yang","year":"2003","unstructured":"Yang OO, Sarkis PT, Ali A, Harlow JD, Brander C, Kalams SA, Walker BD: Determinant of HIV-1 mutational escape from cytotoxic T lymphocytes. J Exp Med. 2003, 197: 1365-1375. 10.1084\/jem.20022138.","journal-title":"J Exp Med"},{"key":"1678_CR13","doi-asserted-by":"crossref","DOI":"10.56021\/9780801861505","volume-title":"The Evolution of HIV","author":"KA Crandall","year":"1999","unstructured":"Crandall KA: The Evolution of HIV. 1999, Baltimore, MD: The Johns Hopkins University Press"},{"key":"1678_CR14","doi-asserted-by":"publisher","first-page":"529","DOI":"10.1084\/jem.20052116","volume":"203","author":"R Draenert","year":"2006","unstructured":"Draenert R, Allen TM, Liu Y, Wrin T, Chappey C, Verrill CL, Sirera G, Eldridge RL, Lahaie MP, Ruiz L, et al: Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus. J Exp Med. 2006, 203: 529-539. 10.1084\/jem.20052116.","journal-title":"J Exp Med"},{"key":"1678_CR15","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1084\/jem.20060216","volume":"203","author":"DH O'Connor","year":"2006","unstructured":"O'Connor DH, Burton DR: Immune responses and HIV: a little order from the chaos. J Exp Med. 2006, 203: 501-503.","journal-title":"J Exp Med"},{"key":"1678_CR16","doi-asserted-by":"publisher","first-page":"15368","DOI":"10.1128\/JVI.79.24.15368-15375.2005","volume":"79","author":"OO Yang","year":"2005","unstructured":"Yang OO, Church J, Kitchen CM, Kilpatrick R, Ali A, Geng Y, Killian MS, Sabado RL, Ng H, Suen J, et al: Genetic and stochastic influences on the interaction of human immunodeficiency virus type 1 and cytotoxic T lymphocytes in identical twins. J Virol. 2005, 79: 15368-15375. 10.1128\/JVI.79.24.15368-15375.2005.","journal-title":"J Virol"},{"key":"1678_CR17","doi-asserted-by":"publisher","first-page":"12666","DOI":"10.1128\/JVI.01450-07","volume":"81","author":"XG Yu","year":"2007","unstructured":"Yu XG, Lichterfeld M, Williams KL, Martinez-Picado J, Walker BD: Random T-cell receptor recruitment in human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells from genetically identical twins infected with the same HIV-1 strain. J Virol. 2007, 81: 12666-12669. 10.1128\/JVI.01450-07.","journal-title":"J Virol"},{"key":"1678_CR18","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1146\/annurev.genet.36.040202.111115","volume":"36","author":"D Posada","year":"2002","unstructured":"Posada D, Crandall KA, Holmes EC: Recombination in evolutionary genomics. Annu Rev Genet. 2002, 36: 75-97. 10.1146\/annurev.genet.36.040202.111115.","journal-title":"Annu Rev Genet"},{"key":"1678_CR19","first-page":"129","volume":"5","author":"RF Schinazi","year":"1997","unstructured":"Schinazi RF, Larder BA, Mellors JW: Mutations in retroviral genes associated with drug resistance. Int Antiviral News. 1997, 5: 129-142.","journal-title":"Int Antiviral News"},{"key":"1678_CR20","doi-asserted-by":"publisher","first-page":"6700","DOI":"10.1073\/pnas.0901855106","volume":"106","author":"M Nozawa","year":"2009","unstructured":"Nozawa M, Suzuki Y, Nei M: Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA. 2009, 106: 6700-6705. 10.1073\/pnas.0901855106.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1678_CR21","doi-asserted-by":"publisher","first-page":"E95","DOI":"10.1073\/pnas.0904550106","volume":"106","author":"Z Yang","year":"2009","unstructured":"Yang Z, Nielsen R, Goldman N: In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA. 2009, 106: E95-10.1073\/pnas.0904550106.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1678_CR22","doi-asserted-by":"publisher","first-page":"1586","DOI":"10.1093\/molbev\/msm088","volume":"24","author":"Z Yang","year":"2007","unstructured":"Yang Z: PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007, 24: 1586-1591. 10.1093\/molbev\/msm088.","journal-title":"Mol Biol Evol"},{"key":"1678_CR23","doi-asserted-by":"publisher","first-page":"372","DOI":"10.1093\/oxfordjournals.molbev.a026118","volume":"16","author":"KA Crandall","year":"1999","unstructured":"Crandall KA, Kelsey CR, Imamichi H, Salzman NP: Parallel evolution of drug resistance in HIV: failure of nonsynonymous\/synonymous substitution rate ratio to detect selection. Mol Biol Evol. 1999, 16: 372-382.","journal-title":"Mol Biol Evol"},{"key":"1678_CR24","doi-asserted-by":"publisher","first-page":"110","DOI":"10.1016\/j.meegid.2007.10.009","volume":"8","author":"A Carvajal-Rodriguez","year":"2008","unstructured":"Carvajal-Rodriguez A, Posada D, Perez-Losada M, Keller E, Abrams EJ, Viscidi RP, Crandall KA: Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol. 2008, 8: 110-120. 10.1016\/j.meegid.2007.10.009.","journal-title":"Infect Genet Evol"},{"key":"1678_CR25","doi-asserted-by":"publisher","first-page":"10604","DOI":"10.1073\/pnas.0500398102","volume":"102","author":"MF Fraga","year":"2005","unstructured":"Fraga MF, Ballestar E, Paz MF, Ropero S, Setien F, Ballestar ML, Heine-Suner D, Cigudosa JC, Urioste M, Benitez J, et al: Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci USA. 2005, 102: 10604-10609. 10.1073\/pnas.0500398102.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1678_CR26","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1093\/hmg\/ddi116","volume":"14","author":"AH Wong","year":"2005","unstructured":"Wong AH, Gottesman II, Petronis A: Phenotypic differences in genetically identical organisms: the epigenetic perspective. Hum Mol Genet. 2005, 14: 11-18. 10.1093\/hmg\/ddi116.","journal-title":"Hum Mol Genet"},{"key":"1678_CR27","doi-asserted-by":"publisher","first-page":"1862","DOI":"10.1073\/pnas.94.5.1862","volume":"94","author":"AJ Leigh Brown","year":"1997","unstructured":"Leigh Brown AJ: Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc Natl Acad Sci USA. 1997, 94: 1862-1865. 10.1073\/pnas.94.5.1862.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1678_CR28","doi-asserted-by":"publisher","first-page":"719","DOI":"10.2307\/2408026","volume":"34","author":"AR Templeton","year":"1980","unstructured":"Templeton AR: Modes of speciation and inferences based on genetic distances. Evolution. 1980, 34: 719-729. 10.2307\/2408026.","journal-title":"Evolution"},{"key":"1678_CR29","doi-asserted-by":"publisher","first-page":"228","DOI":"10.1016\/0169-5347(90)90137-3","volume":"5","author":"HL Carson","year":"1990","unstructured":"Carson HL: Increased genetic variance after a population bottleneck. Trends Ecol Evol. 1990, 5: 228-230. 10.1016\/0169-5347(90)90137-3.","journal-title":"Trends Ecol Evol"},{"key":"1678_CR30","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1203\/pdr.0b013e31803c7b98","volume":"61","author":"P Poulsen","year":"2007","unstructured":"Poulsen P, Esteller M, Vaag A, Fraga MF: The epigenetic basis of twin discordance in age-related diseases. Pediatr Res. 2007, 61: 38-42. 10.1203\/pdr.0b013e31803c7b98.","journal-title":"Pediatr Res"},{"key":"1678_CR31","doi-asserted-by":"publisher","first-page":"7552","DOI":"10.1073\/pnas.0802203105","volume":"105","author":"BF Keele","year":"2008","unstructured":"Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, et al: Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci USA. 2008, 105: 7552-7557. 10.1073\/pnas.0802203105.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1678_CR32","first-page":"1","volume":"10","author":"C Hay","year":"1998","unstructured":"Hay C, Rosenberg E: Immunologic response to HIV. AIDS Clin Care. 1998, 10: 1-3.","journal-title":"AIDS Clin Care"},{"key":"1678_CR33","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1371\/journal.pmed.0050100","volume":"5","author":"H Streeck","year":"2008","unstructured":"Streeck H, Brumme ZL, Anastario M, Cohen KW, Jolin JS, Meier A, Brumme CJ, Rosenberg ES, Alter G, Allen TM, et al: Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells. PLoS Med. 2008, 5: e100-10.1371\/journal.pmed.0050100.","journal-title":"PLoS Med"},{"key":"1678_CR34","doi-asserted-by":"publisher","first-page":"9216","DOI":"10.1128\/JVI.01041-08","volume":"82","author":"ZL Brumme","year":"2008","unstructured":"Brumme ZL, Brumme CJ, Carlson J, Streeck H, John M, Eichbaum Q, Block BL, Baker B, Kadie C, Markowitz M, et al: Marked epitope- and allele-specific differences in rates of mutation in human immunodeficiency type 1 (HIV-1) Gag, Pol, and Nef cytotoxic T-lymphocyte epitopes in acute\/early HIV-1 infection. J Virol. 2008, 82: 9216-9227. 10.1128\/JVI.01041-08.","journal-title":"J Virol"},{"key":"1678_CR35","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1093\/nar\/gki198","volume":"33","author":"K Katoh","year":"2005","unstructured":"Katoh K, Kuma K, Toh H, Miyata T: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 2005, 33: 511-518. 10.1093\/nar\/gki198.","journal-title":"Nucleic Acids Res"},{"key":"1678_CR36","volume-title":"MacClade 4: Analysis of Phylogeny and Character Evolution, version 4.0","author":"DR Maddison","year":"2000","unstructured":"Maddison DR, Maddison WP: MacClade 4: Analysis of Phylogeny and Character Evolution, version 4.0. 2000, Sinauer Associates"},{"key":"1678_CR37","doi-asserted-by":"publisher","first-page":"368","DOI":"10.1007\/BF01734359","volume":"17","author":"J Felsenstein","year":"1981","unstructured":"Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981, 17: 368-376. 10.1007\/BF01734359.","journal-title":"J Mol Evol"},{"key":"1678_CR38","doi-asserted-by":"publisher","first-page":"783","DOI":"10.2307\/2408678","volume":"39","author":"J Felsenstein","year":"1985","unstructured":"Felsenstein J: Confidence limits on phylogenies: an approach using the bootstrap. Evolution. 1985, 39: 783-791. 10.2307\/2408678.","journal-title":"Evolution"},{"key":"1678_CR39","doi-asserted-by":"publisher","first-page":"696","DOI":"10.1080\/10635150390235520","volume":"52","author":"S Guindon","year":"2003","unstructured":"Guindon S, Gascuel O: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003, 52: 696-704. 10.1080\/10635150390235520.","journal-title":"Syst Biol"},{"key":"1678_CR40","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1080\/10635150290102366","volume":"51","author":"JP Huelsenbeck","year":"2002","unstructured":"Huelsenbeck JP, Larget B, Miller RE, Ronquist F: Potential applications and pitfalls of Bayesian inference of phylogeny. Syst Biol. 2002, 51: 673-688. 10.1080\/10635150290102366.","journal-title":"Syst Biol"},{"key":"1678_CR41","doi-asserted-by":"publisher","first-page":"1572","DOI":"10.1093\/bioinformatics\/btg180","volume":"19","author":"F Ronquist","year":"2003","unstructured":"Ronquist F, Huelsenbeck JP: MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003, 19: 1572-1574. 10.1093\/bioinformatics\/btg180.","journal-title":"Bioinformatics"},{"key":"1678_CR42","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1080\/10635150490522304","volume":"53","author":"D Posada","year":"2004","unstructured":"Posada D, Buckley TR: Model selection and model averaging in phylogenetics: Advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst Biol. 2004, 53: 793-808. 10.1080\/10635150490522304.","journal-title":"Syst Biol"},{"key":"1678_CR43","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1093\/bioinformatics\/14.9.817","volume":"14","author":"D Posada","year":"1998","unstructured":"Posada D, Crandall KA: MODELTEST: testing the model of DNA substitution. Bioinformatics. 1998, 14: 817-818. 10.1093\/bioinformatics\/14.9.817.","journal-title":"Bioinformatics"},{"key":"1678_CR44","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","volume":"19","author":"A Hirotugu","year":"1974","unstructured":"Hirotugu A: A new look at the statistical model identification. IEEE Transact Automatic Control. 1974, 19: 716-723. 10.1109\/TAC.1974.1100705.","journal-title":"IEEE Transact Automatic Control"},{"key":"1678_CR45","volume-title":"Tracer: MCMC trace analysis tool. 1.4.1 edition","author":"A Rambaut","year":"2009","unstructured":"Rambaut A, Drummond AJ: Tracer: MCMC trace analysis tool. 1.4.1 edition. 2009, Edinburgh: Institute of Evolutionary Biology, [ http:\/\/tree.bio.ed.ac.uk\/software\/tracer\/ ]"},{"key":"1678_CR46","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1093\/genetics\/132.2.619","volume":"132","author":"AR Templeton","year":"1992","unstructured":"Templeton AR, Crandall KA, Sing CF: A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics. 1992, 132: 619-633.","journal-title":"Genetics"},{"key":"1678_CR47","doi-asserted-by":"publisher","first-page":"1657","DOI":"10.1046\/j.1365-294x.2000.01020.x","volume":"9","author":"M Clement","year":"2000","unstructured":"Clement M, Posada D, Crandall KA: TCS: a computer program to estimate gene genealogies. Mol Ecol. 2000, 9: 1657-1659. 10.1046\/j.1365-294x.2000.01020.x.","journal-title":"Mol Ecol"},{"key":"1678_CR48","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1093\/bioinformatics\/btk051","volume":"22","author":"MK Kuhner","year":"2006","unstructured":"Kuhner MK: LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics. 2006, 22: 768-770. 10.1093\/bioinformatics\/btk051.","journal-title":"Bioinformatics"},{"key":"1678_CR49","doi-asserted-by":"publisher","first-page":"1185","DOI":"10.1093\/molbev\/msi103","volume":"22","author":"AJ Drummond","year":"2005","unstructured":"Drummond AJ, Rambaut A, Shapiro B, Pybus OG: Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol. 2005, 22: 1185-1192. 10.1093\/molbev\/msi103.","journal-title":"Mol Biol Evol"},{"key":"1678_CR50","doi-asserted-by":"publisher","first-page":"e88","DOI":"10.1371\/journal.pbio.0040088","volume":"4","author":"AJ Drummond","year":"2006","unstructured":"Drummond AJ, Ho SY, Phillips MJ, Rambaut A: Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006, 4: e88-10.1371\/journal.pbio.0040088.","journal-title":"PLoS Biol"},{"key":"1678_CR51","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1186\/1471-2148-7-214","volume":"7","author":"AJ Drummond","year":"2007","unstructured":"Drummond AJ, Rambaut A: BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007, 7: 214-10.1186\/1471-2148-7-214.","journal-title":"BMC Evol Biol"},{"key":"1678_CR52","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1093\/genetics\/148.3.929","volume":"148","author":"R Nielsen","year":"1998","unstructured":"Nielsen R, Yang Z: Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 1998, 148: 929-936.","journal-title":"Genetics"},{"key":"1678_CR53","doi-asserted-by":"publisher","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","volume":"21","author":"SL Kosakovsky Pond","year":"2005","unstructured":"Kosakovsky Pond SL, Frost SDW: Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics. 2005, 21: 2531-2533. 10.1093\/bioinformatics\/bti320.","journal-title":"Bioinformatics"},{"key":"1678_CR54","doi-asserted-by":"publisher","first-page":"1208","DOI":"10.1093\/molbev\/msi105","volume":"22","author":"SL Kosakovsky Pond","year":"2005","unstructured":"Kosakovsky Pond SL, Frost SDW: Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection. Mol Biol Evol. 2005, 22: 1208-1222. 10.1093\/molbev\/msi105.","journal-title":"Mol Biol Evol"},{"key":"1678_CR55","doi-asserted-by":"publisher","first-page":"1891","DOI":"10.1093\/molbev\/msl051","volume":"23","author":"SL Kosakovsky Pond","year":"2006","unstructured":"Kosakovsky Pond SL, Posada D, Gravenor MB, Woelk CH, Frost SDW: Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm. Mol Biol Evol. 2006, 23: 1891-1901. 10.1093\/molbev\/msl051.","journal-title":"Mol Biol Evol"}],"container-title":["BMC Evolutionary Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2148-11-62.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2148-11-62\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2148-11-62.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,5]],"date-time":"2023-06-05T17:26:22Z","timestamp":1685985982000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcevolbiol.biomedcentral.com\/articles\/10.1186\/1471-2148-11-62"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,3,8]]},"references-count":55,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2011,12]]}},"alternative-id":["1678"],"URL":"https:\/\/doi.org\/10.1186\/1471-2148-11-62","relation":{},"ISSN":["1471-2148"],"issn-type":[{"value":"1471-2148","type":"electronic"}],"subject":[],"published":{"date-parts":[[2011,3,8]]},"article-number":"62"}}