{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T16:32:05Z","timestamp":1761237125005},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"5","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: We propose a stepwise approach to identify recombination breakpoints in a sequence alignment. The approach can be applied to any recombination detection method that uses a permutation test and provides estimates of breakpoints.<\/jats:p>\n               <jats:p>Results: We illustrate the approach by analyses of a simulated dataset and alignments of real data from HIV-1 and human chromosome 7. The presented simulation results compare the statistical properties of one-step and two-step procedures. More breakpoints are found with a two-step procedure than with a single application of a given method, particularly for higher recombination rates. At higher recombination rates, the additional breakpoints were located at the cost of only a slight increase in the number of falsely declared breakpoints. However, a large proportion of breakpoints still go undetected.<\/jats:p>\n               <jats:p>Availability: A makefile and C source code for phylogenetic profiling and the maximum \u03c72 method, tested with the gcc compiler on Linux and WindowsXP, are available at http:\/\/stat-db.stat.sfu.ca\/stepwise\/<\/jats:p>\n               <jats:p>Contact: \u00a0jgraham@stat.sfu.ca<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti040","type":"journal-article","created":{"date-parts":[[2004,9,24]],"date-time":"2004-09-24T00:15:47Z","timestamp":1095984947000},"page":"589-595","source":"Crossref","is-referenced-by-count":13,"title":["Stepwise detection of recombination breakpoints in sequence alignments"],"prefix":"10.1093","volume":"21","author":[{"given":"Jinko","family":"Graham","sequence":"first","affiliation":[]},{"given":"Brad","family":"McNeney","sequence":"additional","affiliation":[]},{"given":"Fran\u00e7oise","family":"Seillier-Moiseiwitsch","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2004,9,23]]},"reference":[{"key":"2023013107211735100_B1","doi-asserted-by":"crossref","unstructured":"Anderson, J., Rodrigo, A., Learn, G., Madan, A., Delahunty, C., Coon, M., Girard, M., Osmanov, S., Hood, L., Mullins, J. 2000Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. J. Virol.7410752\u201310765","DOI":"10.1128\/JVI.74.22.10752-10765.2000"},{"key":"2023013107211735100_B2","doi-asserted-by":"crossref","unstructured":"Brown, A.J. 1997Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc. Natl Acad. Sci. USA941862\u20131865","DOI":"10.1073\/pnas.94.5.1862"},{"key":"2023013107211735100_B3","unstructured":"Brown, C., Garner, E., Dunker, K., Joyce, P. 2001The power to detect recombination using the coalescent. Mol. Biol. Evol.181421\u20131424"},{"key":"2023013107211735100_B4","unstructured":"Daly, M., Rioux, J.D., Schnaffner, F., Hudson, T., Lander, E.S. 2001High-resolution haplotype structure in the human genome. Nat. Genet.29229\u2013232"},{"key":"2023013107211735100_B5","doi-asserted-by":"crossref","unstructured":"DuBose, R., Dykhuisen, D., Hartl, D. 1988Genetic exchange among natural isolates of bacteria: recombination within the phoa locus of Escherichia coli               . Proc. Natl Acad. Sci. USA857036\u20137040","DOI":"10.1073\/pnas.85.18.7036"},{"key":"2023013107211735100_B6","doi-asserted-by":"crossref","unstructured":"Fang, G., Weiser, B., Kuiken, C., Philpott, S., Rowland-Jones, S., Plummer, F., Kimani, J., Shi, B., Kaul, R., Bwayo, J., Anzala, O., Burger, H. 2004Recombination following superinfection by HIV-1. AIDS18153\u2013159","DOI":"10.1097\/00002030-200401230-00003"},{"key":"2023013107211735100_B7","unstructured":"Fearnhead, P. and Donnelly, P. 2001Estimating recombination rates from population genetic data. Genetics1591299\u20131318"},{"key":"2023013107211735100_B8","unstructured":"Grassly, N. and Holmes, E. 1997A likelihood method for the detection of selection and recombination using nucleotide sequences. Mol. Biol. Evol.14239\u2013247"},{"key":"2023013107211735100_B9","unstructured":"Griffiths, R. and Marjoram, P. 1996Ancestral inference from samples of DNA sequences with recombination. J. Comput. Biol.3479\u2013502"},{"key":"2023013107211735100_B10","doi-asserted-by":"crossref","unstructured":"Griffiths, R. and Marjoram, P. 1997An ancestral recombination graph. In Donnelly, P. and Tavar\u00e9, S. (Eds.). Progress in Population Genetics and Human Evolution , Berlin  IMA Volumes in Mathematics and its Applications Vol. 87 Springer-Verlag,  pp. 257\u2013270","DOI":"10.1007\/978-1-4757-2609-1_16"},{"key":"2023013107211735100_B11","doi-asserted-by":"crossref","unstructured":"Groenink, M., Andeweg, A., Fouchier, R., Broersen, S., van der Jagt, R., Schuitemaker, H., de Goede, R., Bosch, M., Huisman, H., Tersmette, M. 1992Phenotype-associated env gene variation among eight i related human immunodeficiency virus type 1 clones: evidence for in vivo recombination and determinants of cytotropism outside the V3 domain. J. Virol.666175\u20136180","DOI":"10.1128\/jvi.66.10.6175-6180.1992"},{"key":"2023013107211735100_B12","unstructured":"Hudson, R. 1983Properties of a neutral allele model with intragenic recombination. Theoret. Popul. Biol.23183\u2013201"},{"key":"2023013107211735100_B13","unstructured":"Hudson, R. and Kaplan, N. 1985Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics111147\u2013164"},{"key":"2023013107211735100_B14","unstructured":"Hudson, R., Boos, D., Kaplan, N. 1992A statistical test for detecting geographic subdivision. Mol. Biol. Evol.9138\u2013151"},{"key":"2023013107211735100_B15","doi-asserted-by":"crossref","unstructured":"Kuhner, M., Yamato, J., Felsenstein, J. 2000Maximum likelihood estimation of recombination rates from population data. Genetics1561393\u20131410","DOI":"10.1093\/genetics\/156.3.1393"},{"key":"2023013107211735100_B16","doi-asserted-by":"crossref","unstructured":"Leitner, T., Escanilla, D., Marquina, S., Wahlberg, J., Brostrom, C., Hansson, H., Uhlen, M., Albert, J. 1995Biological and molecular characterization of subtype D, G, and {A\/D} recombinant HIV-1 transmissions in Sweden. Virology209136\u2013146","DOI":"10.1006\/viro.1995.1237"},{"key":"2023013107211735100_B17","doi-asserted-by":"crossref","unstructured":"Mansky, L. and Temin, H. 1995Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol.695087\u20135094","DOI":"10.1128\/jvi.69.8.5087-5094.1995"},{"key":"2023013107211735100_B18","unstructured":"McGraw, E., Li, J., Selander, R., Whittam, T. 1999Molecular evolution and mosaic structure of \u03b1, \u03b2, and \u03b3 intimins of pathogenic Escherichia coli               . Mol. Biol. Evol.1612\u201322"},{"key":"2023013107211735100_B19","unstructured":"Myers, S. and Griffiths, R. 2003Bounds on the minimum number of recombination events in a sample history. Genetics163375\u2013394"},{"key":"2023013107211735100_B20","unstructured":"Nielsen, R. 2000Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics154931\u2013942"},{"key":"2023013107211735100_B21","unstructured":"Posada, D. 2002Evaluation of methods for detecting recombination from DNA sequences: Empirical data. Mol. Biol. Evol.19708\u2013717"},{"key":"2023013107211735100_B22","doi-asserted-by":"crossref","unstructured":"Posada, D. and Crandall, K. 2001Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc. Natl Acad. Sci. USA9813757\u201313762","DOI":"10.1073\/pnas.241370698"},{"key":"2023013107211735100_B23","unstructured":"Posada, D., Crandall, K., Holmes, E. 2002Recombination in evolutionary genomics. Annu. Rev. Genet.3675\u201397"},{"key":"2023013107211735100_B24","doi-asserted-by":"crossref","unstructured":"Poss, M., Rodrigo, A., Gosink, J., Learn, G., De Vange Panteleeff, D., Martin, H., Jr, Bwayo, J., Kreiss, J., Overbaugh, J. 1998Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1. J. Virol.728240\u20138251","DOI":"10.1128\/JVI.72.10.8240-8251.1998"},{"key":"2023013107211735100_B25","unstructured":"Rodr\u00edgues, F., Oliver, J., Mar\u00edn, A., Medina, J. 1990The general stochastic model of nucleotide substitution. J. Theoret. Biol.142485\u2013501"},{"key":"2023013107211735100_B26","unstructured":"Sawyer, S. 1989Statistical tests for detecting gene conversion. Mol. Biol. Evol.6526\u2013538"},{"key":"2023013107211735100_B27","unstructured":"Schierup, M.H. and Hein, J. 2000Consequences of recombination on traditional phylogenetic analysis. Genetics156879\u2013891"},{"key":"2023013107211735100_B28","doi-asserted-by":"crossref","unstructured":"Smith, J.M. 1992Analyzing the mosaic structure of genes. J. Mol. Evol.34126\u2013129","DOI":"10.1007\/BF00182389"},{"key":"2023013107211735100_B29","unstructured":"Stephens, M. and Donnelly, P. 2003A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet.731162\u20131169"},{"key":"2023013107211735100_B30","unstructured":"Stephens, M., Smith, N.J., Donnelly, P. 2001A new statistical method for haplotype reconstruction from population data. Am. J. Hum. Genet.68978\u2013989"},{"key":"2023013107211735100_B31","unstructured":"Tavar\u00e9, S. 1986Some probabilistic and statistical problems in the analysis of DNA sequences. In Miura, R. (Ed.). Lectures on Mathematics in the Life Sciences , Providence, RI  American Mathematical Society,  pp. 455\u2013486"},{"key":"2023013107211735100_B32","unstructured":"Weiller, G. 1998Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences. Mol. Biol. Evol.15326\u2013335"},{"key":"2023013107211735100_B33","unstructured":"Wiuf, C., Christensen, T., Hein, J. 2001A simulation study of the reliability of recombination detection methods. Mol. Biol. Evol.181929\u20131939"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/5\/589\/48962322\/bioinformatics_21_5_589.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/5\/589\/48962322\/bioinformatics_21_5_589.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:00:42Z","timestamp":1675159242000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/5\/589\/220009"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,9,23]]},"references-count":33,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2005,3,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bti040","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,3,1]]},"published":{"date-parts":[[2004,9,23]]}}}