{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T07:44:55Z","timestamp":1768463095123,"version":"3.49.0"},"reference-count":69,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2009,11,26]],"date-time":"2009-11-26T00:00:00Z","timestamp":1259193600000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1000581","type":"journal-article","created":{"date-parts":[[2009,11,26]],"date-time":"2009-11-26T01:04:13Z","timestamp":1259197453000},"page":"e1000581","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":156,"title":["An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1"],"prefix":"10.1371","volume":"5","author":[{"given":"Sergei L.","family":"Kosakovsky Pond","sequence":"first","affiliation":[]},{"given":"David","family":"Posada","sequence":"additional","affiliation":[]},{"given":"Eric","family":"Stawiski","sequence":"additional","affiliation":[]},{"given":"Colombe","family":"Chappey","sequence":"additional","affiliation":[]},{"given":"Art F.Y.","family":"Poon","sequence":"additional","affiliation":[]},{"given":"Gareth","family":"Hughes","sequence":"additional","affiliation":[]},{"given":"Esther","family":"Fearnhill","sequence":"additional","affiliation":[]},{"given":"Mike B.","family":"Gravenor","sequence":"additional","affiliation":[]},{"given":"Andrew J.","family":"Leigh Brown","sequence":"additional","affiliation":[]},{"given":"Simon D.W.","family":"Frost","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,11,26]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"16152","DOI":"10.1073\/pnas.0705366104","article-title":"Protein stability imposes limits on organism complexity and speed of molecular evolution.","volume":"104","author":"KB Zeldovich","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"2354","DOI":"10.1126\/science.1070441","article-title":"Diversity considerations in HIV-1 vaccine selection.","volume":"296","author":"B Gaschen","year":"2002","journal-title":"Science"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1126\/science.288.5463.55d","article-title":"HIV-1 nomenclature proposal.","volume":"288","author":"DL Robertson","year":"2000","journal-title":"Science"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"W13","DOI":"10.1097\/01.aids.0000247564.73009.bc","article-title":"Global and regional distribution of HIV-1 genetic subtypes and recombinants in 2004.","volume":"20","author":"J Hemelaar","year":"2006","journal-title":"AIDS"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"13050","DOI":"10.1128\/JVI.00889-07","article-title":"Phylogenetic surveillance of viral genetic diversity and the evolving molecular epidemiology of human immunodeficiency virus type 1.","volume":"81","author":"RJ Gifford","year":"2007","journal-title":"J Virol"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1023\/A:1023435429841","article-title":"Evolution and diversity of HIV-1 in africa\u2013a review.","volume":"26","author":"MA Papathanasopoulos","year":"2003","journal-title":"Virus Genes"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"11193","DOI":"10.1128\/JVI.77.20.11193-11200.2003","article-title":"High rates of human immunodeficiency virus type 1 recombination: near-random segregation of markers one kilobase apart in one round of viral replication.","volume":"77","author":"T Rhodes","year":"2003","journal-title":"J Virol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"8543","DOI":"10.1128\/JVI.00463-07","article-title":"Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form.","volume":"81","author":"AB Abecasis","year":"2007","journal-title":"J Virol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"13757","DOI":"10.1073\/pnas.241370698","article-title":"Evaluation of methods for detecting recombination from DNA sequences: Computer simulations.","volume":"98","author":"D Posada","year":"2001","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1093\/oxfordjournals.molbev.a004129","article-title":"Evaluation of methods for detecting recombination from dna sequences: empirical data.","volume":"19","author":"D Posada","year":"2002","journal-title":"Mol Biol Evol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"1423","DOI":"10.1089\/aid.1995.11.1423","article-title":"Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.","volume":"11","author":"M Salminen","year":"1995","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1089\/088922200309485","article-title":"Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K.","volume":"16","author":"K Triques","year":"2000","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"885","DOI":"10.1089\/0889222041725172","article-title":"Drug resistance testing provides evidence of the globalization of HIV type 1: a new circulating recombinant form.","volume":"20","author":"M Gomez-Carrillo","year":"2004","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1089\/aid.2005.21.98","article-title":"A modified bootscan algorithm for automated identification of recombinant sequences and recombination breakpoints.","volume":"21","author":"DP Martin","year":"2005","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"10234","DOI":"10.1128\/JVI.72.12.10234-10241.1998","article-title":"An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I).","volume":"72","author":"F Gao","year":"1998","journal-title":"J Virol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1099\/0022-1317-82-3-575","article-title":"Re-analysis of human immunodeficiency virus type 1 isolates from Cyprus and Greece, initially designated \u2018subtype I\u2019, reveals a unique complex A\/G\/H\/K\/? mosaic pattern.","volume":"82","author":"D Paraskevis","year":"2001","journal-title":"J Gen Virol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"532","DOI":"10.1097\/01.qai.0000186363.27587.c0","article-title":"Identification of a novel HIV-1 circulating ADG intersubtype recombinant form (CRF19_cpx) in Cuba.","volume":"40","author":"G Casado","year":"2005","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3797","DOI":"10.1093\/bioinformatics\/bti607","article-title":"An automated genotyping system for analysis of HIV-1 and other microbial sequences.","volume":"21","author":"T de Oliveira","year":"2005","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1744","DOI":"10.1093\/bioinformatics\/btm248","article-title":"Nucleotide composition string selection in HIV-1 subtyping using whole genomes.","volume":"23","author":"X Wu","year":"2007","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"W654","DOI":"10.1093\/nar\/gkh419","article-title":"A web-based genotyping resource for viral sequences.","volume":"32","author":"M Rozanov","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"3535","DOI":"10.1093\/bioinformatics\/bti569","article-title":"A statistical model for HIV-1 sequence classification using the subtype analyser (STAR).","volume":"21","author":"RE Myers","year":"2005","journal-title":"Bioinformatics"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1186\/1471-2105-7-265","article-title":"A jumping profile Hidden Markov Model and applications to recombination sites in HIV and HCV genomes.","volume":"7","author":"AK Schultz","year":"2006","journal-title":"BMC Bioinformatics"},{"key":"ref23","article-title":"Limitations in using online tools to determine HIV-1 subtype in clinical patients: A comparison of 5 tools.","author":"C Loveday","year":"2006"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"995","DOI":"10.1089\/aid.2008.0064","article-title":"Discrepancies in assignment of subtype\/recombinant forms by genotyping programs for HIV type 1 drug resistance testing may falsely predict superinfection.","volume":"24","author":"M Ntemgwa","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"3896","DOI":"10.1128\/JCM.00515-08","article-title":"Reliability of rapid subtyping tools compared to that of phylogenetic analysis for characterization of human immunodeficiency virus type 1 non-B subtypes and recombinant forms.","volume":"46","author":"A Holguin","year":"2008","journal-title":"J Clin Microbiol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1521","DOI":"10.1097\/01.aids.0000237368.64488.ae","article-title":"Assessment of automated genotyping protocols as tools for surveillance of HIV-1 genetic diversity.","volume":"20","author":"R Gifford","year":"2006","journal-title":"AIDS"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"396","DOI":"10.1007\/s00239-001-0034-9","article-title":"The effect of recombination on the accuracy of phylogeny estimation.","volume":"54","author":"D Posada","year":"2002","journal-title":"J Mol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3034","DOI":"10.1093\/bioinformatics\/bti459","article-title":"Dual multiple change-point model leads to more accurate recombination detection.","volume":"21","author":"VN Minin","year":"2005","journal-title":"Bioinformatics"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1891","DOI":"10.1093\/molbev\/msl051","article-title":"Automated phylogenetic detection of recombination using a genetic algorithm.","volume":"23","author":"SL Kosakovsky Pond","year":"2006","journal-title":"Mol Biol Evol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.","volume":"21","author":"SL Kosakovsky Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref31","first-page":"57","article-title":"Some probabilistic and statistical problems in the analysis of DNA sequences.","volume":"17","author":"S Tavar\u00e9","year":"1986","journal-title":"Lectures on Mathematics in the Life Sciences"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1093\/molbev\/msi009","article-title":"A simple hierarchical approach to modeling distributions of substitution rates.","volume":"22","author":"S Kosakovsky Pond","year":"2005","journal-title":"Mol Biol Evol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/bti191","article-title":"RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.","volume":"21","author":"A Stamatakis","year":"2005","journal-title":"Bioinformatics"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the dimension of a model.","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Stat"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"716","DOI":"10.1109\/TAC.1974.1100705","article-title":"A new look at the statistical model identification.","volume":"119","author":"H Akaike","year":"1974","journal-title":"IEEE Tran Automatic Control"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1080\/03610927808827599","article-title":"Further analysis of the data by Akaike&apos;s information criterion and the finite corrections.","volume":"A7","author":"N Sugiura","year":"1978","journal-title":"Communications In Statistics-Theory And Methods"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1007\/s002390010105","article-title":"Maximum likelihood estimation on large phylogenies and analysis of adaptive evolution in human influenza virus A.","volume":"51","author":"ZH Yang","year":"2000","journal-title":"J Mol Evol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1007\/BF01734359","article-title":"Evolutionary trees from DNA sequences: a maximum likelihood approach.","volume":"17","author":"J Felsenstein","year":"1981","journal-title":"J Mol Evol"},{"key":"ref40","article-title":"FOGA-1, Los Atlos, CA: Morgan Kaufmann, chapter The CHC adaptive search algorithm. How to have safe search when engaging in nontraditional genetic recombination.","volume":"265-283","author":"L Eshelman","year":"1991"},{"key":"ref41","article-title":"Genetic algorithms in search, optimization, and machine learning.","author":"DE Goldberg","year":"1989"},{"key":"ref42","article-title":"Model Selection and Multimodel Inference.","author":"K Burnham","year":"2003"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"890","DOI":"10.1093\/oxfordjournals.molbev.a026369","article-title":"A fast algorithm for joint reconstruction of ancestral amino acid sequences.","volume":"17","author":"T Pupko","year":"2000","journal-title":"Mol Biol Evol"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"443","DOI":"10.1016\/0022-2836(70)90057-4","article-title":"A general method applicable to the search for similarities in the amino acid sequence of two proteins.","volume":"48","author":"SB Needleman","year":"1970","journal-title":"J Mol Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"e503","DOI":"10.1371\/journal.pone.0000503","article-title":"HIV-specific probabilistic models of protein evolution.","volume":"2","author":"DC Nickle","year":"2007","journal-title":"PLoS ONE"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1126\/science.1151532","article-title":"Alignment uncertainty and genomic analysis.","volume":"319","author":"KM Wong","year":"2008","journal-title":"Science"},{"key":"ref47","first-page":"512","article-title":"Estimation of the number of nucleotide substitutions in the control region of mitochondrial-DNA in humans and chimpanzees.","volume":"10","author":"K Tamura","year":"1993","journal-title":"Mol Biol Evol"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1089\/aid.2007.0181","article-title":"The HIV type 1 epidemic in Bulgaria involves multiple subtypes and is sustained by continuous viral inflow from West and East European countries.","volume":"24","author":"M Salemi","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"e4724","DOI":"10.1371\/journal.pone.0004724","article-title":"Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update.","volume":"4","author":"DE Bennett","year":"2009","journal-title":"PLoS One"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/bti079","article-title":"HyPhy: hypothesis testing using phylogenies.","volume":"21","author":"SL Kosakovsky Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref51","first-page":"138","article-title":"Update of the drug resistance mutations in HIV-1.","volume":"16","author":"VA Johnson","year":"2008","journal-title":"Top HIV Med"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1056\/NEJMoa013552","article-title":"Antiretroviral-drug resistance among patients recently infected with HIV.","volume":"347","author":"SJ Little","year":"2002","journal-title":"N Eng J Med"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1097\/01.qai.0000219290.49152.6a","article-title":"Tracking the prevalence of transmitted antiretroviral drug-resistant HIV-1: a decade of experience.","volume":"41","author":"A Shet","year":"2006","journal-title":"J Acquir Immune Defic Syndr"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1097\/QAD.0b013e3282f47ad0","article-title":"Identification of two new CRF_BF in Rio de Janeiro State, Brazil.","volume":"22","author":"ML Guimaraes","year":"2008","journal-title":"AIDS"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1089\/088922202320886325","article-title":"Among 46 near full length HIV type 1 genome sequences from Rakai District, Uganda, subtype D and AD recombinants predominate.","volume":"18","author":"ME Harris","year":"2002","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"11693","DOI":"10.1128\/JVI.79.18.11693-11704.2005","article-title":"In-depth analysis of a heterosexually acquired human immunodeficiency virus type 1 superinfection: evolution, temporal fluctuation, and intercompartment dynamics from the seronegative window period through 30 months postinfection.","volume":"79","author":"FE McCutchan","year":"2005","journal-title":"J Virol"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1976","DOI":"10.1093\/oxfordjournals.molbev.a003738","article-title":"Unveiling the molecular clock in the presence of recombination.","volume":"18","author":"D Posada","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1093\/bioinformatics\/btl427","article-title":"Robust inference of positive selection from recombining coding sequences.","volume":"22","author":"K Scheffler","year":"2006","journal-title":"Bioinformatics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1089\/aid.2007.0183","article-title":"HIV subtypes induce distinct profiles of HIV-specific CD8(+) T cell responses.","volume":"24","author":"CAR Baker","year":"2008","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"e1000214","DOI":"10.1371\/journal.pcbi.1000214","article-title":"Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.","volume":"4","author":"O Penn","year":"2008","journal-title":"PLoS Comput Biol"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"4492","DOI":"10.1128\/JVI.02050-06","article-title":"Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.","volume":"81","author":"CM Rousseau","year":"2007","journal-title":"J Virol"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1016\/j.ympev.2008.08.017","article-title":"An exploratory algorithm to identify intra-host recombinant viral sequences.","volume":"49","author":"M Salemi","year":"2008","journal-title":"Mol Phylogenet Evol"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1015","DOI":"10.1089\/08892220050058434","article-title":"HIV type 1 A\/J recombinant with a pronounced pol gene mosaicism.","volume":"16","author":"VA Novitsky","year":"2000","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1089\/aid.1995.11.427","article-title":"At least five HIV-1 sequence subtypes (A, B, C, D, A\/E) occur in England.","volume":"11","author":"C Arnold","year":"1995","journal-title":"AIDS Res Hum Retroviruses"},{"key":"ref65","article-title":"Health Protection Report 2007."},{"key":"ref66","doi-asserted-by":"crossref","first-page":"4425","DOI":"10.1073\/pnas.0407534102","article-title":"Genetic analysis reveals the complex structure of HIV-1 transmission within defined risk groups.","volume":"102","author":"S Hue","year":"2005","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"707","DOI":"10.1086\/527416","article-title":"Effect of human immunodeficiency virus Type 1 (HIV-1) subtype on disease progression in persons from Rakai, Uganda, with incident HIV-1 infection.","volume":"197","author":"N Kiwanuka","year":"2008","journal-title":"J Infect Dis"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1097\/01.qco.0000200293.45532.68","article-title":"HIV-1 subtypes: epidemiology and significance for HIV management.","volume":"19","author":"AM Geretti","year":"2006","journal-title":"Curr Opin Infect Dis"},{"key":"ref69","doi-asserted-by":"crossref","first-page":"1296","DOI":"10.1086\/598502","article-title":"Effect of HIV-1 subtype on virologic and immunologic response to starting highly active antiretroviral therapy.","volume":"48","author":"AM Geretti","year":"2009","journal-title":"Clin Infect Dis"}],"container-title":["PLoS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000581","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,23]],"date-time":"2020-05-23T22:08:29Z","timestamp":1590271709000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1000581"}},"subtitle":[],"editor":[{"given":"Christophe","family":"Fraser","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,11,26]]},"references-count":69,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2009,11,26]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1000581","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,11,26]]}}}