메뉴 건너뛰기




Volumn 25, Issue 19, 2009, Pages 2530-2536

Improving phylogenetic analyses by incorporating additional information from genetic sequence databases

Author keywords

[No Author keywords available]

Indexed keywords

ENOLASE;

EID: 70349878973     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp473     Document Type: Article
Times cited : (6)

References (30)
  • 1
    • 33845381928 scopus 로고    scopus 로고
    • The posterior and the prior in Bayesian phylogenetics
    • Alfaro,M. and Holder,M. (2006) The posterior and the prior in Bayesian phylogenetics. Ann. Rev. Ecol. Evol. Syst., 37, 19-42.
    • (2006) Ann. Rev. Ecol. Evol. Syst , vol.37 , pp. 19-42
    • Alfaro, M.1    Holder, M.2
  • 2
    • 0036273056 scopus 로고    scopus 로고
    • The potential value of indels as phylogenetic markers: Position of trichomonads as a case study
    • Bapteste,E. and Philippe,H. (2002) The potential value of indels as phylogenetic markers: Position of trichomonads as a case study. Mol. Biol. Evol., 19, 972-977.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 972-977
    • Bapteste, E.1    Philippe, H.2
  • 3
    • 0030327054 scopus 로고    scopus 로고
    • A new perspective on priors for generalized linear models
    • Bedrick,E.J. et al. (1996) A new perspective on priors for generalized linear models. J. Am. Stat. Assoc., 91, 1450-1460.
    • (1996) J. Am. Stat. Assoc , vol.91 , pp. 1450-1460
    • Bedrick, E.J.1
  • 4
    • 0031531928 scopus 로고    scopus 로고
    • Bayesian binomial regression: Predicting survival at a trauma center
    • Bedrick,E.J. et al. (1997) Bayesian binomial regression: predicting survival at a trauma center. Am. Stat., 51, 211-218.
    • (1997) Am. Stat , vol.51 , pp. 211-218
    • Bedrick, E.J.1
  • 5
    • 0002617436 scopus 로고
    • Ferguson distributions via polya urn schemes
    • Blackwell,D. and MacQueen,J.B. (1973) Ferguson distributions via polya urn schemes. Ann. Stat., 1, 353-355.
    • (1973) Ann. Stat , vol.1 , pp. 353-355
    • Blackwell, D.1    MacQueen, J.B.2
  • 7
    • 0000904732 scopus 로고    scopus 로고
    • A semiparametric Bayesian model for randomised block designs
    • Bush,C.A. and MacEachern,S.N. (1996) A semiparametric Bayesian model for randomised block designs. Biometrika, 83, 275-285.
    • (1996) Biometrika , vol.83 , pp. 275-285
    • Bush, C.A.1    MacEachern, S.N.2
  • 9
    • 0442277964 scopus 로고    scopus 로고
    • Empirical Bayes: Past, present, and future
    • Carlin,B.P. and Louis,T. (2000) Empirical Bayes: Past, present, and future. J. Am. Stat. Assoc., 95, 1286-1289.
    • (2000) J. Am. Stat. Assoc , vol.95 , pp. 1286-1289
    • Carlin, B.P.1    Louis, T.2
  • 10
    • 0347568778 scopus 로고    scopus 로고
    • Empirical Bayes methods for combining likelihoods
    • Efron,B. (1996) Empirical Bayes methods for combining likelihoods. J. Am. Stat. Assoc., 91, 538-550.
    • (1996) J. Am. Stat. Assoc , vol.91 , pp. 538-550
    • Efron, B.1
  • 11
    • 84950937290 scopus 로고
    • Bayesian density estimation and inference using mixtures
    • Escobar,M.D. and West,M. (1995) Bayesian density estimation and inference using mixtures. J. Am. Stat. Assoc., 90, 577-588.
    • (1995) J. Am. Stat. Assoc , vol.90 , pp. 577-588
    • Escobar, M.D.1    West, M.2
  • 12
    • 84950453304 scopus 로고
    • Sampling-based approaches to calculating marginal densities
    • Gelfand,A.E. and Smith,A.F.M. (1990) Sampling-based approaches to calculating marginal densities. J. Am. Stat. Assoc., 85, 398-409.
    • (1990) J. Am. Stat. Assoc , vol.85 , pp. 398-409
    • Gelfand, A.E.1    Smith, A.F.M.2
  • 13
    • 0004012196 scopus 로고    scopus 로고
    • 2nd edn. Chapman & Hall/CRC, Boca Raton, FL
    • Gelman,A. et al. (2003) Bayesian Data Analysis, 2nd edn. Chapman & Hall/CRC, Boca Raton, FL.
    • (2003) Bayesian Data Analysis
    • Gelman, A.1
  • 14
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck,J.P. and Ronquist,F. (2001) MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics, 17, 754-755.
    • (2001) Bioinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 16
    • 35748954378 scopus 로고    scopus 로고
    • Effect of branch length uncertainty on posterior probabilities for phylogenetic hypotheses
    • Kolaczkowski,B. and Thornton,J. (2007) Effect of branch length uncertainty on posterior probabilities for phylogenetic hypotheses. Mol. Biol. Evol., 24, 2108-2118.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 2108-2118
    • Kolaczkowski, B.1    Thornton, J.2
  • 17
    • 0025905252 scopus 로고
    • The order of sequence alignment can bias the selection of tree topology
    • Lake,J. (1991) The order of sequence alignment can bias the selection of tree topology. Mol. Biol. Evol., 8, 378-385.
    • (1991) Mol. Biol. Evol , vol.8 , pp. 378-385
    • Lake, J.1
  • 18
    • 34548378755 scopus 로고    scopus 로고
    • A hierarchical semi-parametric regression model for combining HIV-1 phylogenetic analyses using iterative reweighting algorithms
    • Liang,L. and Weiss,R. (2007) A hierarchical semi-parametric regression model for combining HIV-1 phylogenetic analyses using iterative reweighting algorithms. Biometrics, 63, 733-741.
    • (2007) Biometrics , vol.63 , pp. 733-741
    • Liang, L.1    Weiss, R.2
  • 19
    • 0030487956 scopus 로고    scopus 로고
    • Nonparametric hierarchical bayes via sequential imputations
    • Liu,J. (1996) Nonparametric hierarchical bayes via sequential imputations. Ann. Stat., 24, 911-930.
    • (1996) Ann. Stat , vol.24 , pp. 911-930
    • Liu, J.1
  • 20
    • 84950432453 scopus 로고
    • Parametric empirical Bayes inference: Theory and application
    • Morris,C. (1983) Parametric empirical Bayes inference: Theory and application. J. Am. Stat. Assoc., 78, 47-59.
    • (1983) J. Am. Stat. Assoc , vol.78 , pp. 47-59
    • Morris, C.1
  • 21
    • 0036803348 scopus 로고    scopus 로고
    • Identifiability of parameters in MCMC Bayesian inference of phylogeny
    • Rannala,B. (2002) Identifiability of parameters in MCMC Bayesian inference of phylogeny. Syst. Biol., 51, 754-760.
    • (2002) Syst. Biol , vol.51 , pp. 754-760
    • Rannala, B.1
  • 22
    • 22844450838 scopus 로고    scopus 로고
    • Joint Bayesian estimation of alignment and phylogeny
    • Redelings,B. and Suchard,M. (2005) Joint Bayesian estimation of alignment and phylogeny. Syst. Biology, 54, 401-418.
    • (2005) Syst. Biology , vol.54 , pp. 401-418
    • Redelings, B.1    Suchard, M.2
  • 23
    • 34247340566 scopus 로고    scopus 로고
    • Incorporating indel information into phylogeny estimation for rapidly emerging pathogens
    • Redelings,B. and Suchard,M. (2007) Incorporating indel information into phylogeny estimation for rapidly emerging pathogens. BMC Evol. Biol. 7, 40.
    • (2007) BMC Evol. Biol , vol.7 , pp. 40
    • Redelings, B.1    Suchard, M.2
  • 25
    • 0000720609 scopus 로고
    • A constructive definition of Dirichlet priors
    • Sethurman,J. (1994) A constructive definition of Dirichlet priors. Stat. Sin., 4, 639-650.
    • (1994) Stat. Sin , vol.4 , pp. 639-650
    • Sethurman, J.1
  • 26
    • 33747863926 scopus 로고    scopus 로고
    • BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny
    • Suchard,M. and Redelings,B. (2006) BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics, 22, 2047-2048.
    • (2006) Bioinformatics , vol.22 , pp. 2047-2048
    • Suchard, M.1    Redelings, B.2
  • 27
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson,J. et al. (1999) BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics, 15, 87-88.
    • (1999) Bioinformatics , vol.15 , pp. 87-88
    • Thompson, J.1
  • 28
    • 0000576595 scopus 로고
    • Markov chains for exploring posterior distributions
    • Tierney,L. (1994) Markov chains for exploring posterior distributions. Ann. Stat., 22, 1701-1762.
    • (1994) Ann. Stat , vol.22 , pp. 1701-1762
    • Tierney, L.1
  • 29
    • 22844452772 scopus 로고    scopus 로고
    • Branch-length prior influences Bayesian posterior probability of phylogeny
    • Yang,Z. and Rannala,B. (2005) Branch-length prior influences Bayesian posterior probability of phylogeny. Syst. Biol., 54, 455-470.
    • (2005) Syst. Biol , vol.54 , pp. 455-470
    • Yang, Z.1    Rannala, B.2
  • 30
    • 70349870661 scopus 로고    scopus 로고
    • Model parameterization, prior distributions and the general time-reversible model in Bayesian phylogenetics
    • Zwickl,D. and Holder,M. (2004) Model parameterization, prior distributions and the general time-reversible model in Bayesian phylogenetics. Syst. Biol., 54, 961-965.
    • (2004) Syst. Biol , vol.54 , pp. 961-965
    • Zwickl, D.1    Holder, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.