메뉴 건너뛰기




Volumn 62, Issue 1, 2010, Pages 145-159

Distribution of distances between topologies and its effect on detection of phylogenetic recombination

Author keywords

Markov chain Monte Carlo; Phylogenetics; SPR distance; Viral recombination

Indexed keywords

BIOLOGICAL SEQUENCE DATA; CENTROID METHOD; DATA SETS; EVOLUTIONARY HISTORY; EVOLUTIONARY MODELS; EXISTING METHOD; HIERARCHICAL BAYESIAN; MARKOV CHAIN MONTE CARLO; MOSAIC STRUCTURE; PHYLOGENETICS;

EID: 77950692373     PISSN: 00203157     EISSN: 15729052     Source Type: Journal    
DOI: 10.1007/s10463-009-0259-8     Document Type: Article
Times cited : (3)

References (30)
  • 1
    • 0016355478 scopus 로고
    • A new look at the statistical model identification
    • Akaike, H. (1974). A new look at the statistical model identification. IEEE Transactions on Automatic Control, 19(6), 716-723.
    • (1974) IEEE Transactions on Automatic Control , vol.19 , Issue.6 , pp. 716-723
    • Akaike, H.1
  • 2
    • 4344653003 scopus 로고    scopus 로고
    • Improving the acceptance rate of reversible jump MCMC proposals
    • Al-Awadhi, F., Hurn, M., Jennison, C. (2004). Improving the acceptance rate of reversible jump MCMC proposals. Statistics and Probability Letters, 69(2), 189-198.
    • (2004) Statistics and Probability Letters , vol.69 , Issue.2 , pp. 189-198
    • Al-Awadhi, F.1    Hurn, M.2    Jennison, C.3
  • 3
    • 0347512294 scopus 로고    scopus 로고
    • Subtree transfer operations and their induced metrics on evolutionary trees
    • Allen, B., Steel, M. (2001). Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics, 5(1), 1-15.
    • (2001) Annals of Combinatorics , vol.5 , Issue.1 , pp. 1-15
    • Allen, B.1    Steel, M.2
  • 4
    • 1342309210 scopus 로고    scopus 로고
    • Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference
    • Altekar, G., Dwarkadas, S., Huelsenbeck, J. P., Ronquist, F. (2004). Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics, 20(3), 407-415.
    • (2004) Bioinformatics , vol.20 , Issue.3 , pp. 407-415
    • Altekar, G.1    Dwarkadas, S.2    Huelsenbeck, J.P.3    Ronquist, F.4
  • 5
    • 0037223888 scopus 로고    scopus 로고
    • The evolutionary genomics of pathogen recombination
    • Awadalla, P. (2003). The evolutionary genomics of pathogen recombination. Nature Reviews Genetics, 4(1), 50-60.
    • (2003) Nature Reviews Genetics , vol.4 , Issue.1 , pp. 50-60
    • Awadalla, P.1
  • 6
    • 33645568886 scopus 로고    scopus 로고
    • Phylogenetic identification of lateral genetic transfer events
    • Beiko, R. G., Hamilton, N. (2006). Phylogenetic identification of lateral genetic transfer events. BMC Evolutionary Biology, 6, 15.
    • (2006) BMC Evolutionary Biology , vol.6 , pp. 15
    • Beiko, R.G.1    Hamilton, N.2
  • 7
    • 42149083815 scopus 로고    scopus 로고
    • Centroid estimation in discrete high-dimensional spaces with applications in biology
    • Carvalho, L. E., Lawrence, C. E. (2008). Centroid estimation in discrete high-dimensional spaces with applications in biology. Proceedings of the National Academy of Sciences USA, 105(9), 3209-3214.
    • (2008) Proceedings of the National Academy of Sciences USA , vol.105 , Issue.9 , pp. 3209-3214
    • Carvalho, L.E.1    Lawrence, C.E.2
  • 8
    • 0010045457 scopus 로고    scopus 로고
    • Bayesian curve-fitting with free-knot splines
    • Dimatteo, I., Genovese, C., Kass, R. (2001). Bayesian curve-fitting with free-knot splines. Biometrika, 88(4), 1055-1071.
    • (2001) Biometrika , vol.88 , Issue.4 , pp. 1055-1071
    • Dimatteo, I.1    Genovese, C.2    Kass, R.3
  • 9
    • 23644448438 scopus 로고    scopus 로고
    • Rna secondary structure prediction by centroids in a boltzmann weighted ensemble
    • Ding,Y.,Chan, C.Y.,Lawrence, C. E. (2005).Rna secondary structure prediction by centroids in a boltzmann weighted ensemble. RNA, 11(8), 1157-1166.
    • (2005) RNA , vol.11 , Issue.8 , pp. 1157-1166
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 10
    • 33847312870 scopus 로고    scopus 로고
    • CBrother: Relaxing parental tree assumptions for Bayesian recombination detection
    • Fang, F., Ding, J., Minin, V. N., Suchard, M. A., Dorman, K. S. (2007). cBrother: relaxing parental tree assumptions for Bayesian recombination detection. Bioinformatics, 23(4), 507-508.
    • (2007) Bioinformatics , vol.23 , Issue.4 , pp. 507-508
    • Fang, F.1    Ding, J.2    Minin, V.N.3    Suchard, M.A.4    Dorman, K.S.5
  • 11
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein, J. (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution, 17(6), 368-376.
    • (1981) Journal of Molecular Evolution , vol.17 , Issue.6 , pp. 368-376
    • Felsenstein, J.1
  • 15
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa, M., Kishino, H., Yano, T. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22(2), 160-174.
    • (1985) Journal of Molecular Evolution , vol.22 , Issue.2 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.3
  • 17
    • 21444455535 scopus 로고    scopus 로고
    • Dual multiple change-point model leads to more accurate recombination detection
    • Minin, V. N., Dorman, K. S., Fang, F., Suchard, M. A. (2005). Dual multiple change-point model leads to more accurate recombination detection. Bioinformatics, 21(13), 3034-3042.
    • (2005) Bioinformatics , vol.21 , Issue.13 , pp. 3034-3042
    • Minin, V.N.1    Dorman, K.S.2    Fang, F.3    Suchard, M.A.4
  • 19
    • 50349088009 scopus 로고    scopus 로고
    • Phylogenetic detection of recombination with a Bayesian prior on the distance between trees
    • de Oliveira Martins, L., Leal, É., Kishino, H. (2008). Phylogenetic detection of recombination with a Bayesian prior on the distance between trees. PLoS ONE, 3(7), e2651.
    • (2008) PLoS ONE , vol.3 , Issue.7
    • De Oliveira Martins, L.1    Leal, É.2    Kishino, H.3
  • 20
    • 0036097812 scopus 로고    scopus 로고
    • Evaluation of methods for detecting recombination from dna sequences: Empirical data
    • Posada, D. (2002). Evaluation of methods for detecting recombination from dna sequences: empirical data. Molecular Biology and Evolution, 19, 708-717.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 708-717
    • Posada, D.1
  • 21
    • 9644301241 scopus 로고    scopus 로고
    • Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests
    • Posada, D., Buckley, T. (2004). Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Systematic Biology, 53(5), 793-808.
    • (2004) Systematic Biology , vol.53 , Issue.5 , pp. 793-808
    • Posada, D.1    Buckley, T.2
  • 22
    • 15944402575 scopus 로고    scopus 로고
    • On the combinatorics of rooted binary phylogenetic trees
    • Song, Y. (2003). On the combinatorics of rooted binary phylogenetic trees. Annals of Combinatorics, 7(3), 365-379.
    • (2003) Annals of Combinatorics , vol.7 , Issue.3 , pp. 365-379
    • Song, Y.1
  • 24
    • 0042243482 scopus 로고    scopus 로고
    • Inferring spatial phylogenetic variation along nucleotide sequences: A multiple changepoint model
    • Suchard, M., Weiss, R., Dorman, K., Sinsheimer, J. (2003). Inferring spatial phylogenetic variation along nucleotide sequences: a multiple changepoint model. Journal of the American Statistical Association, 98(462), 427-438.
    • (2003) Journal of the American Statistical Association , vol.98 , Issue.462 , pp. 427-438
    • Suchard, M.1    Weiss, R.2    Dorman, K.3    Sinsheimer, J.4
  • 25
    • 0002671410 scopus 로고
    • Some probabilistic and statistical problems in the analysis of DNA sequences
    • R.M. Miura (Ed.) Providence: AMS Bookstore
    • Tavaré, S. (1986). Some probabilistic and statistical problems in the analysis of DNA sequences. In R.M. Miura (Ed.), Some Mathematical Questions in Biology - DNA Sequence Analysis (pp. 57-86). Providence: AMS Bookstore.
    • (1986) Some Mathematical Questions in Biology - DNA Sequence Analysis , pp. 57-86
    • Tavaré, S.1
  • 26
    • 44949258055 scopus 로고    scopus 로고
    • Measuring global credibility with application to local sequence alignment
    • Webb-Robertson, B. J. M., McCue, L. A., Lawrence, C. E. (2008). Measuring global credibility with application to local sequence alignment. PLoS Computational Biology, 4(5), e1000077.
    • (2008) PLoS Computational Biology , vol.4 , Issue.5
    • Webb-robertson, B.J.M.1    McCue, L.A.2    Lawrence, C.E.3
  • 27
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang, Z. (1993).Maximum-likelihood estimation of phylogeny from dna sequences when substitution rates differ over sites. Molecular Biology and Evolution, 10(6), 1396-1401. (Pubitemid 23352619)
    • (1993) Molecular Biology and Evolution , vol.10 , Issue.6 , pp. 1396-1401
    • Yang, Z.1
  • 28
    • 0028214103 scopus 로고
    • Estimating the pattern of nucleotide substitution
    • Yang, Z. (1994a). Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution, 39(1), 105-111.
    • (1994) Journal of Molecular Evolution , vol.39 , Issue.1 , pp. 105-111
    • Yang, Z.1
  • 29
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: Approximate methods
    • Yang, Z. (1994b). Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: approximate methods. Journal of Molecular Evolution, 39(3), 306-314.
    • (1994) Journal of Molecular Evolution , vol.39 , Issue.3 , pp. 306-314
    • Yang, Z.1
  • 30
    • 34547803197 scopus 로고    scopus 로고
    • Paml 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. (2007). Paml 4: phylogenetic analysis by maximum likelihood. Molecular Biology and Evolution, 24(8), 1586-1591.
    • (2007) Molecular Biology and Evolution , vol.24 , Issue.8 , pp. 1586-1591
    • Yang, Z.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.