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Volumn 2009, Issue 5, 2009, Pages 67-79

A mixture model and a Hidden Markov Model to simultaneously detect recombination breakpoints and reconstruct phylogenies

Author keywords

Maximum likelihood; Molecular phylogeny; PhyML; Recombination

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; COMPUTER PROGRAM; DNA SEQUENCE; EVOLUTIONARY ALGORITHM; GENE SEQUENCE; GENETIC RECOMBINATION; HIDDEN MARKOV MODEL; HOMOLOGOUS RECOMBINATION; NUCLEOTIDE SEQUENCE; PHYLOGENETIC TREE; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 68149165460     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (20)

References (26)
  • 1
    • 0036097812 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from DNA sequences: Empirical data
    • Posada, David. Evaluation of methods for detecting recombination from DNA sequences: empirical data. Mol Biol Evol. 2002;19(5):708-17.
    • (2002) Mol Biol Evol , vol.19 , Issue.5 , pp. 708-717
    • Posada, D.1
  • 2
    • 33646167864 scopus 로고    scopus 로고
    • A simple and robust statistical test for detecting the presence of recombination
    • Bruen, Trevor C, Philippe, Herve, et Bryant, David. A simple and robust statistical test for detecting the presence of recombination. Genetics. 2006;172(4):2665-81.
    • (2006) Genetics , vol.172 , Issue.4 , pp. 2665-2681
    • Bruen, T.C.1    Philippe, H.2    Bryant, D.3
  • 3
    • 0034048880 scopus 로고    scopus 로고
    • A Bayesian model for detecting past recombination events in DNA multiple alignments
    • McGuire G, Wright F, et Prentice MJ. A Bayesian model for detecting past recombination events in DNA multiple alignments. J Comput Biol. 2000;7(1-2):159-70.
    • (2000) J Comput Biol , vol.7 , Issue.1-2 , pp. 159-170
    • McGuire, G.1    Wright, F.2    Prentice, M.J.3
  • 4
    • 0030034795 scopus 로고    scopus 로고
    • A Hidden Markov Model approach to variation among sites in rate of evolution
    • Felsenstein J, et Churchill, GA. A Hidden Markov Model approach to variation among sites in rate of evolution. Mol Biol Evol. 1996;13(1):93-104.
    • (1996) Mol Biol Evol , vol.13 , Issue.1 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.A.2
  • 5
    • 27544493059 scopus 로고    scopus 로고
    • Husmeier, Dirk. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics. 2005;21 Suppl 2Sep; iil66-iil72.
    • Husmeier, Dirk. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics. 2005;21 Suppl 2(Sep; iil66-iil72.
  • 6
    • 18744378862 scopus 로고    scopus 로고
    • Detecting interspecific recombination with a pruned probabilistic divergence measure
    • Husmeier, Dirk, Wright, Frank, et Milne, Iain. Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics. 2005;21(9):1797-806.
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1797-1806
    • Husmeier, D.1    Wright, F.2    Milne, I.3
  • 7
    • 33750367870 scopus 로고    scopus 로고
    • A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion
    • 5: Article27
    • Kedzierska, Anna, et Husmeier, Dirk. A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion. Stat Appl Genet Mol Biol. 2006;5: Article27.
    • (2006) Stat Appl Genet Mol Biol
    • Kedzierska, A.1    Husmeier, D.2
  • 8
    • 0036803331 scopus 로고    scopus 로고
    • Suchard, Marc A, Weiss, et al. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst Biol. 2002;51(5):715-28.
    • Suchard, Marc A, Weiss, et al. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst Biol. 2002;51(5):715-28.
  • 9
    • 85142143285 scopus 로고    scopus 로고
    • Minin, Vladimir N, Dorman, et al. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 2005; 21(13):3034-42.
    • Minin, Vladimir N, Dorman, et al. Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics. 2005; 21(13):3034-42.
  • 10
    • 34249045460 scopus 로고    scopus 로고
    • Minin, Vladimir N, Dorman, et al. Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics. 2007;175(4):1773-85.
    • Minin, Vladimir N, Dorman, et al. Phylogenetic mapping of recombination hotspots in human immunodeficiency virus via spatially smoothed change-point processes. Genetics. 2007;175(4):1773-85.
  • 11
    • 85142177725 scopus 로고    scopus 로고
    • Pond, Sergei L Kosakovsky, et al. GARD: a genetic algorithm for recombination detection. Bioinformatics. 2006b;22(24):3096-8.
    • Pond, Sergei L Kosakovsky, et al. GARD: a genetic algorithm for recombination detection. Bioinformatics. 2006b;22(24):3096-8.
  • 12
    • 33748770095 scopus 로고    scopus 로고
    • Pond, Sergei L Kosakovsky, et al. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 2006a; 23(10):1891-901.
    • Pond, Sergei L Kosakovsky, et al. Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol. 2006a; 23(10):1891-901.
  • 13
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, et Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987; 4(4):406-25.
    • (1987) Mol Biol Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 14
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol. 1981;17(6):368-76.
    • (1981) J Mol Evol , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 15
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, Stephane, et Gascuel, Olivier. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 2003;52(5):696-704.
    • (2003) Syst Biol , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 16
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel O. BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol. 1997;14(7):685-95.
    • (1997) Mol Biol Evol , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 17
    • 84959042115 scopus 로고    scopus 로고
    • Gueguen, Laurent. Segmentation by maximal predictive partitioning according to composition biases. Chap. Segmentation by maximal predictive partitioning according to composition biases., pages 32-45 of: O, Gascuel, et M, Sagot (eds), Computational Biology. LNCS, 2066. Springer-Verlag. 2001.
    • Gueguen, Laurent. Segmentation by maximal predictive partitioning according to composition biases. Chap. Segmentation by maximal predictive partitioning according to composition biases., pages 32-45 of: O, Gascuel, et M, Sagot (eds), Computational Biology. LNCS, vol. 2066. Springer-Verlag. 2001.
  • 18
    • 24044463584 scopus 로고    scopus 로고
    • Sarment: Python modules for HMM analysis and partitioning of sequences
    • Gueguen, Laurent. Sarment: Python modules for HMM analysis and partitioning of sequences. Bioinformatics. 2005;21(16):3427-8.
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3427-3428
    • Gueguen, L.1
  • 19
    • 84945709924 scopus 로고
    • On the approximation of curves by line segments using dynamic programming
    • Bellman, Richard. On the approximation of curves by line segments using dynamic programming. j-CACM. 1961;4(6):284-284.
    • (1961) j-CACM , vol.4 , Issue.6 , pp. 284-284
    • Bellman, R.1
  • 20
    • 68149093361 scopus 로고    scopus 로고
    • Robinson D, et Foulds L. Comparaison of weighted labeled tree. Pages 119-126 of: A.F. Horadam, et Wallis, WD (eds), Isomorphic factorisations VI: Automorphisms, combinatorial mathematics. Lecture Notes in Mathematics, no. 748. Springer, Berlin. 1979.
    • Robinson D, et Foulds L. Comparaison of weighted labeled tree. Pages 119-126 of: A.F. Horadam, et Wallis, WD (eds), Isomorphic factorisations VI: Automorphisms, combinatorial mathematics. Lecture Notes in Mathematics, no. 748. Springer, Berlin. 1979.
  • 21
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A, et Grassly NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 1997;13(3):235-238.
    • (1997) Comput Appl Biosci , vol.13 , Issue.3 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 22
    • 0021277009 scopus 로고
    • A new method for calculating evolutionary substitution rates
    • Lanave C, Preparata G, Saccone C, et Serio G. A new method for calculating evolutionary substitution rates. J Mol Evol. 1984;20(1):86-93.
    • (1984) J Mol Evol , vol.20 , Issue.1 , pp. 86-93
    • Lanave, C.1    Preparata, G.2    Saccone, C.3    Serio, G.4
  • 23
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M, Kishino H, et Yano T. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol. 1985;22(2):160-74.
    • (1985) J Mol Evol , vol.22 , Issue.2 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 24
    • 33749613832 scopus 로고    scopus 로고
    • Chan, Cheong Xin, Beiko, Robert G, et Ragan, Mark A. Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics. 2006;7:412.
    • Chan, Cheong Xin, Beiko, Robert G, et Ragan, Mark A. Detecting recombination in evolving nucleotide sequences. BMC Bioinformatics. 2006;7:412.
  • 25
    • 0036623258 scopus 로고    scopus 로고
    • An approximately unbiased test of phylogenetic tree selection
    • Shimodaira H. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 2002;51(3):492-508.
    • (2002) Syst Biol , vol.51 , Issue.3 , pp. 492-508
    • Shimodaira, H.1
  • 26
    • 50349088009 scopus 로고    scopus 로고
    • de Oliveira Martins, Leonardo, Leal, Elcio, et Kishino, Hirohisa. Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS ONE. 2008;3(7):e2651.
    • de Oliveira Martins, Leonardo, Leal, Elcio, et Kishino, Hirohisa. Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS ONE. 2008;3(7):e2651.


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