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Volumn 32, Issue 2, 2004, Pages 495-503

A comparison of methods for estimating the transition:transversion ratio from DNA sequences

Author keywords

Bayesian estimation; Independent contrasts; Maximum likelihood; Rate variation; Transition bias; Transition transversion ratio

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; DNA SEQUENCE; EVALUATION; GENETICS; METHODOLOGY; MOLECULAR EVOLUTION; MUTATION; PHYLOGENY; POINT MUTATION;

EID: 3042686794     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ympev.2004.01.013     Document Type: Article
Times cited : (18)

References (25)
  • 1
    • 0002943417 scopus 로고
    • Comparative methods using phylogenetically independent contrasts
    • Burt A. Comparative methods using phylogenetically independent contrasts. Oxford Surv. Evol. Biol. 1989;33-53
    • (1989) Oxford Surv. Evol. Biol. , pp. 33-53
    • Burt, A.1
  • 2
    • 0026757412 scopus 로고
    • Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: A showcase for the molecular evolution of DNA viruses
    • Chan S.-Y., Bernard H.-U., Ong C.-K., Chan S.-P., Hoffman B., Delius H. Phylogenetic analysis of 48 papillomavirus types and 28 subtypes and variants: a showcase for the molecular evolution of DNA viruses. J. Virol. 66:1992;5714-5725
    • (1992) J. Virol. , vol.66 , pp. 5714-5725
    • Chan, S.-Y.1    Bernard, H.-U.2    Ong, C.-K.3    Chan, S.-P.4    Hoffman, B.5    Delius, H.6
  • 3
    • 0028926716 scopus 로고
    • Analysis of genomic sequences of 95 papillomavirus types: Uniting typing, phylogeny, and taxonomy
    • Chan S.-Y., Delius H., Halpern A., Bernard H.-U. Analysis of genomic sequences of 95 papillomavirus types: uniting typing, phylogeny, and taxonomy. J. Virol. 69:1995;3074-3082
    • (1995) J. Virol. , vol.69 , pp. 3074-3082
    • Chan, S.-Y.1    Delius, H.2    Halpern, A.3    Bernard, H.-U.4
  • 4
    • 0021581577 scopus 로고
    • Distance methods for inferring phylogenies: A justification
    • Felsenstein J. Distance methods for inferring phylogenies: a justification. Evolution. 38:1984;16-24
    • (1984) Evolution , vol.38 , pp. 16-24
    • Felsenstein, J.1
  • 5
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa M., Kishino H., Yano T.-A. Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21:1985;160-174
    • (1985) J. Mol. Evol. , vol.21 , pp. 160-174
    • Hasegawa, M.1    Kishino, H.2    Yano, T.-A.3
  • 6
    • 0024120079 scopus 로고
    • Molecular phylogeny and evolution of primate mitochondrial DNA
    • Hayasaka K., Gojobori T., Horai S. Molecular phylogeny and evolution of primate mitochondrial DNA. Mol. Biol. Evol. 5:1988;626-644
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 626-644
    • Hayasaka, K.1    Gojobori, T.2    Horai, S.3
  • 7
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck J., Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics. 17:2001;754-755
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.1    Ronquist, F.2
  • 8
    • 0031954283 scopus 로고    scopus 로고
    • Estimation of the transition/transversion ratio
    • Ina Y. Estimation of the transition/transversion ratio. J. Mol. Evol. 46:1998;521-528
    • (1998) J. Mol. Evol. , vol.46 , pp. 521-528
    • Ina, Y.1
  • 9
    • 0036435298 scopus 로고    scopus 로고
    • Molecular phylogeny of 48 species of damselfishes (Perciformes: Pomacentridae) using 12S mtDNA sequences
    • Jang-Liaw N.-H., Tang K., Hui C.-F., Shao K.-T. Molecular phylogeny of 48 species of damselfishes (Perciformes: Pomacentridae) using 12S mtDNA sequences. Mol. Phyl. Evol. 25:2002;445-454
    • (2002) Mol. Phyl. Evol. , vol.25 , pp. 445-454
    • Jang-Liaw, N.-H.1    Tang, K.2    Hui, C.-F.3    Shao, K.-T.4
  • 10
    • 1542532208 scopus 로고    scopus 로고
    • Phylogenetic tree construction using Markov Chain Monte Carlo
    • Li S., Pearl D., Doss H. Phylogenetic tree construction using Markov Chain Monte Carlo. J. Am. Stat. Assoc. 95:2000;493-508
    • (2000) J. Am. Stat. Assoc. , vol.95 , pp. 493-508
    • Li, S.1    Pearl, D.2    Doss, H.3
  • 11
    • 0032906031 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference via Markov Chain Monte Carlo methods
    • Mau B., Newton M., Larget B. Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics. 55:1999;1-12
    • (1999) Biometrics , vol.55 , pp. 1-12
    • Mau, B.1    Newton, M.2    Larget, B.3
  • 12
    • 0031055633 scopus 로고    scopus 로고
    • Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees
    • Ong C.-K., Nee S., Rambaut A., Bernard H.-U., Harvey P.H. Elucidating the population histories and transmission dynamics of papillomaviruses using phylogenetic trees. J. Mol. Evol. 44:1997;199-206
    • (1997) J. Mol. Evol. , vol.44 , pp. 199-206
    • Ong, C.-K.1    Nee, S.2    Rambaut, A.3    Bernard, H.-U.4    Harvey, P.H.5
  • 13
    • 0029065148 scopus 로고
    • A comparison of two methods for reconstructing evolutionary distances from a weighted contribution of transition and transversion differences
    • Pollock D.B., Goldstein D.D. A comparison of two methods for reconstructing evolutionary distances from a weighted contribution of transition and transversion differences. Mol. Biol. Evol. 12:1995;713-717
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 713-717
    • Pollock, D.B.1    Goldstein, D.D.2
  • 14
    • 0031015213 scopus 로고    scopus 로고
    • Estimating the transition/transversion ratio from independent comparisons with an assumed phylogeny
    • Purvis A., Bromham L. Estimating the transition/transversion ratio from independent comparisons with an assumed phylogeny. J. Mol. Evol. 44:1997;112-119
    • (1997) J. Mol. Evol. , vol.44 , pp. 112-119
    • Purvis, A.1    Bromham, L.2
  • 15
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut A., Grassly N. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:1997;235-238
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.2
  • 16
    • 0003658925 scopus 로고    scopus 로고
    • Cary, NC
    • SAS Institute Inc. 2002. SAS Version 8, Cary, NC
    • (2002) SAS Version 8
  • 18
    • 0028297534 scopus 로고
    • Substitution-rate variation among sites and the estimation of transition bias
    • Wakeley J. Substitution-rate variation among sites and the estimation of transition bias. Mol. Biol. Evol. 11:1994;436-442
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 436-442
    • Wakeley, J.1
  • 19
    • 0001062055 scopus 로고    scopus 로고
    • The excess of transitions among nucleotide substitutions: New methods of estimating transition bias underscore its significance
    • Wakeley J. The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore its significance. TREE. 11:1996;158-163
    • (1996) TREE , vol.11 , pp. 158-163
    • Wakeley, J.1
  • 20
    • 1842869297 scopus 로고    scopus 로고
    • Estimation of evolutionary parameters with phylogenetic trees
    • Wang Q., Salter L.A., Pearl D.K. Estimation of evolutionary parameters with phylogenetic trees. J. Mol. Evol. 55:2002;684-695
    • (2002) J. Mol. Evol. , vol.55 , pp. 684-695
    • Wang, Q.1    Salter, L.A.2    Pearl, D.K.3
  • 22
    • 0028267146 scopus 로고
    • Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation
    • Yang Z., Goldman N., Friday A. Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol. 11:1994;316-324
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 316-324
    • Yang, Z.1    Goldman, N.2    Friday, A.3
  • 23
    • 0029892459 scopus 로고    scopus 로고
    • Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
    • Yang Z., Kumar S. Approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites. Mol. Biol. Evol. 13:1996;650-659
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 650-659
    • Yang, Z.1    Kumar, S.2
  • 24
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
    • Yang Z., Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14:1997;717-724
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.1    Rannala, B.2
  • 25
    • 0033004740 scopus 로고    scopus 로고
    • Estimation of the transition/transversion rate bias and species sampling
    • Yang Z., Yoder A. Estimation of the transition/transversion rate bias and species sampling. J. Mol. Evol. 48:1999;274-283
    • (1999) J. Mol. Evol. , vol.48 , pp. 274-283
    • Yang, Z.1    Yoder, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.