메뉴 건너뛰기




Volumn 4, Issue 4, 2003, Pages 275-284

Phylogeny estimation: Traditional and Bayesian approaches

Author keywords

[No Author keywords available]

Indexed keywords

BAYES THEOREM; COMPUTER PROGRAM; GENE SEQUENCE; GENETIC VARIABILITY; HUMAN; HYPOTHESIS; MAXIMUM LIKELIHOOD METHOD; MONTE CARLO METHOD; NATURAL SELECTION; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; REVIEW; TAXONOMY;

EID: 0037379673     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1044     Document Type: Review
Times cited : (461)

References (68)
  • 1
    • 0033639150 scopus 로고    scopus 로고
    • Statistical methods for detecting molecular adaptation
    • Yang, Z. & Bielawski, J. P. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15, 496-502 (2000)
    • (2000) Trends Ecol. Evol. , vol.15 , pp. 496-502
    • Yang, Z.1    Bielawski, J.P.2
  • 2
    • 0035527347 scopus 로고    scopus 로고
    • Empirical and hierarchical Bayesian estimation of ancestral states
    • Huelsenbeck, J. P. & Bollback, J. P. Empirical and hierarchical Bayesian estimation of ancestral states. Syst. Biol. 50, 351-366 (2001).
    • (2001) Syst. Biol. , vol.50 , pp. 351-366
    • Huelsenbeck, J.P.1    Bollback, J.P.2
  • 3
    • 0037195104 scopus 로고    scopus 로고
    • Molecular evidence of HIV-1 transmission in a criminal case
    • Metzker, M. L. et al. Molecular evidence of HIV-1 transmission in a criminal case. Proc. Natl Acad. Sci. USA 99, 14292-14297 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 14292-14297
    • Metzker, M.L.1
  • 4
    • 0033579329 scopus 로고    scopus 로고
    • Isolation of West Nile virus from mosquitoes, crows, and a Cooper's hawk in Connecticut
    • Anderson, J. F. et al. Isolation of West Nile virus from mosquitoes, crows, and a Cooper's hawk in Connecticut. Science 286, 2331-2333 (1999).
    • (1999) Science , vol.286 , pp. 2331-2333
    • Anderson, J.F.1
  • 5
    • 0033579282 scopus 로고    scopus 로고
    • Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States
    • Lanciotti, R. S. et al. Origin of the West Nile virus responsible for an outbreak of encephalitis in the northeastern United States. Science 286, 2333-2337 (1999).
    • (1999) Science , vol.286 , pp. 2333-2337
    • Lanciotti, R.S.1
  • 6
    • 0001336205 scopus 로고    scopus 로고
    • eds Hillis, D. M., Moritz, C. & Mable, B. K. Sinauer Associates, Sunderland, Massachusetts. An excellent review of parsimony, ML and distance approaches to phylogenetic inference
    • Swofford, D. L. Olsen, G. J., Waddell, P. J. & Hillis, D. M. in Molecular Systematics (eds Hillis, D. M., Moritz, C. & Mable, B. K.) 407-514 (Sinauer Associates, Sunderland, Massachusetts, 1996). An excellent review of parsimony, ML and distance approaches to phylogenetic inference.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 7
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987).
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 8
    • 0024114801 scopus 로고
    • A note on the neighbor-joining algorithm of Saitou and Nei
    • Studier, J. A. & Keppler, K. J. A note on the neighbor-joining algorithm of Saitou and Nei. Mol. Biol. Evol. 5, 729-731 (1988).
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 9
    • 0034035066 scopus 로고    scopus 로고
    • Parsimony, likelihood and the role of models in molecular phylogenetics
    • Steel, M. & Penny, D. Parsimony, likelihood and the role of models in molecular phylogenetics. Mol. Biol. Evol. 16, 839-850 (2000).
    • (2000) Mol. Biol. Evol. , vol.16 , pp. 839-850
    • Steel, M.1    Penny, D.2
  • 11
    • 0033854992 scopus 로고    scopus 로고
    • Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used
    • Takahashi, K. & Nei, M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol. Biol. Evol. 17, 1251-1258 (2000).
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 1251-1258
    • Takahashi, K.1    Nei, M.2
  • 12
    • 84959743928 scopus 로고
    • Methods for computing Wagner trees
    • Farris, J. S. Methods for computing Wagner trees. Syst. Zool. 19, 83-92 (1970).
    • (1970) Syst. Zool. , vol.19 , pp. 83-92
    • Farris, J.S.1
  • 13
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimal change for a specific tree topology
    • Fitch, W. M. Toward defining the course of evolution: minimal change for a specific tree topology. Syst. Zool. 20, 406-416 (1971).
    • (1971) Syst. Zool. , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 14
    • 84963036271 scopus 로고
    • Quantitative phyletics and the evolution of anurans
    • Kluge, A. G. & Farris, J. S. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1-32 (1969).
    • (1969) Syst. Zool. , vol.18 , pp. 1-32
    • Kluge, A.G.1    Farris, J.S.2
  • 15
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27, 401-410 (1978). A seminal paper that reported the phenomenon of long-branch attraction.
    • (1978) Syst. Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 16
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D. M. Inferring complex phylogenies. Nature 383, 130-131 (1996).
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.M.1
  • 17
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • Kim, J. H. General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Syst. Biol. 45, 363-374 (1996).
    • (1996) Syst. Biol. , vol.45 , pp. 363-374
    • Kim, J.H.1
  • 18
    • 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. 17, 368-376 (1981).
    • (1981) J. Mol. Evol. , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 19
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State-of-the-art methods for looking into the past
    • Whelan, S., Lio, P. & Goldman, N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17, 262-272 (2001).
    • (2001) Trends Genet. , vol.17 , pp. 262-272
    • Whelan, S.1    Lio, P.2    Goldman, N.3
  • 20
    • 0004128472 scopus 로고
    • Oxford Univ. Press, Oxford, UK
    • Edwards, A. W. F. Likelihood (Oxford Univ. Press, Oxford, UK, 1972).
    • (1972) Likelihood
    • Edwards, A.W.F.1
  • 21
    • 0032025769 scopus 로고    scopus 로고
    • A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences
    • Rogers, J. S. & Swofford, D. L. A fast method for approximating maximum likelihoods of phylogenetic trees from nucleotide sequences. Syst. Biol. 47, 77-89 (1998).
    • (1998) Syst. Biol. , vol.47 , pp. 77-89
    • Rogers, J.S.1    Swofford, D.L.2
  • 22
    • 0002344794 scopus 로고
    • Bootstrap methods: Another look at the jackknife
    • Efron, B. Bootstrap methods: another look at the jackknife. Annals Stat. 7, 1-26 (1979).
    • (1979) Annals Stat. , vol.7 , pp. 1-26
    • Efron, B.1
  • 23
    • 0000461280 scopus 로고
    • Confidence intervals on phylogenies: An approach using the bootstrap
    • Felsenstein, J. Confidence intervals on phylogenies: an approach using the bootstrap. Evolution 39, 783-791 (1985).
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 24
    • 0034351387 scopus 로고    scopus 로고
    • Likelihood-based tests of topologies in phylogenetics
    • Goldman, N., Anderson, J. P. & Rodrigo, A. G. Likelihood-based tests of topologies in phylogenetics. Syst. Biol. 49, 652-670 (2000). A useful taxonomy of the hypothesis-testing approaches for likelihood-based phylogenetics.
    • (2000) Syst. Biol. , vol.49 , pp. 652-670
    • Goldman, N.1    Anderson, J.P.2    Rodrigo, A.G.3
  • 25
    • 12044253190 scopus 로고
    • An empirical test of bootstrapping as a methods for assessing confidence in phylogenetic analysis
    • Hillis, D. M. & Bull, J. J. An empirical test of bootstrapping as a methods for assessing confidence in phylogenetic analysis. Syst. Biol. 42, 182-192 (1993).
    • (1993) Syst. Biol. , vol.42 , pp. 182-192
    • Hillis, D.M.1    Bull, J.J.2
  • 26
    • 0026443498 scopus 로고
    • Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock
    • Zharkikh, A. & Li, W.-H. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. J. Mol. Evol. 9, 1119-1147 (1992)
    • (1992) J. Mol. Evol. , vol.9 , pp. 1119-1147
    • Zharkikh, A.1    Li, W.-H.2
  • 27
    • 12044259827 scopus 로고
    • Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull
    • Felsenstein, J. & Kishino, H. Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42, 193-200 (1993).
    • (1993) Syst. Biol. , vol.42 , pp. 193-200
    • Felsenstein, J.1    Kishino, H.2
  • 28
    • 0030581603 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • Efron, B., Halloran, E. & Holmes, S. Bootstrap confidence levels for phylogenetic trees. Proc. Natl Acad. Sci. USA 93, 13429-13434 (1996)
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 13429-13434
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 29
    • 0035527406 scopus 로고    scopus 로고
    • Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods
    • Swofford, D. L. et al. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50, 525-539 (2001). A recent contribution to the debate concerning parsimony and likelihood.
    • (2001) Syst. Biol. , vol.50 , pp. 525-539
    • Swofford, D.L.1
  • 30
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J. P., Ronquist, F., Nielsen, R. & Bollback, J. P. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294, 2310-2314 (2001). A discussion of the promise that Bayesian phylogenetics holds for transforming evolutionary biology.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielsen, R.3    Bollback, J.P.4
  • 31
    • 0034849408 scopus 로고    scopus 로고
    • MRBAYES: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. & Ronquist, F. R. MRBAYES: Bayesian inference of phylogenetic trees. Boinformatics 17, 754-755 (2001).
    • (2001) Boinformatics , vol.17 , pp. 754-755
    • Huelsenbeck, J.P.1    Ronquist, F.R.2
  • 32
    • 0032976397 scopus 로고    scopus 로고
    • Markov Chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B. & Simon, D. L. Markov Chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750-759 (1999).
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 33
    • 1542532208 scopus 로고    scopus 로고
    • Phylogenetic tree construction using Markov Chain Monte Carlo
    • Li, S., Pearl, D. K. & Doss, H. Phylogenetic tree construction using Markov Chain Monte Carlo. J. Am. Stat. Assoc. 95, 493-508 (2000)
    • (2000) J. Am. Stat. Assoc. , vol.95 , pp. 493-508
    • Li, S.1    Pearl, D.K.2    Doss, H.3
  • 34
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala, B. & Yang, Z. Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311 (1996).
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 35
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov Chain Monte Carlo method
    • Yang, Z. H. & Rannala, B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14, 717-724 (1997).
    • (1997) Mol. Biol. Evol. , vol.14 , pp. 717-724
    • Yang, Z.H.1    Rannala, B.2
  • 37
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne, J. L., Kishino, H. & Painter, I. S. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15, 1647-1657 (1998).
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 38
    • 0035103260 scopus 로고    scopus 로고
    • Performance of a divergence time estimation method under a probabilistic model of rate evolution
    • Kishino, H., Thorne, J. L. & Bruno, W. J. Performance of a divergence time estimation method under a probabilistic model of rate evolution. Mol. Biol. Evol. 18, 352-361 (2001).
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 352-361
    • Kishino, H.1    Thorne, J.L.2    Bruno, W.J.3
  • 39
    • 0034077901 scopus 로고    scopus 로고
    • A compound Poisson process for relaxing the molecular clock
    • Huelsenbeck, J. P., Larget, B. & Swofford, D. L. A compound Poisson process for relaxing the molecular clock. Genetics 154, 1879-1892 (2000).
    • (2000) Genetics , vol.154 , pp. 1879-1892
    • Huelsenbeck, J.P.1    Larget, B.2    Swofford, D.L.3
  • 40
    • 0036804729 scopus 로고    scopus 로고
    • Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    • Aris-Brosou, S. & Yang, Z. Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny. Syst. Biol. 51, 703-714 (2002).
    • (2002) Syst. Biol. , vol.51 , pp. 703-714
    • Aris-Brosou, S.1    Yang, Z.2
  • 41
    • 0002331493 scopus 로고
    • eds Kasha, M. & Pullman, B. Academic Press, New York
    • Zuckerkandl, E. & Pauling, L. In Horizons in Biochemistry (eds Kasha, M. & Pullman, B.) 189-225 (Academic Press, New York, 1962).
    • (1962) Horizons in Biochemistry , pp. 189-225
    • Zuckerkandl, E.1    Pauling, L.2
  • 42
    • 0033790132 scopus 로고    scopus 로고
    • Geometry of phylogenetic estimation
    • Kim, J. Geometry of phylogenetic estimation. Mol. Phylogenet. Evol. 17, 58-75 (2000).
    • (2000) Mol. Phylogenet. Evol. , vol.17 , pp. 58-75
    • Kim, J.1
  • 43
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings, W. K. Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57, 97-109 (1970).
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 44
    • 5744249209 scopus 로고
    • Equation of state calculations by fast computing machines
    • Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., Teller, A. H. & Teller, E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21, 1087-1092 (1953). References 43 and 44 present the Metropolis-Hastings algorithm that is the underpinning of many implementations of MCMC.
    • (1953) J. Chem. Phys. , vol.21 , pp. 1087-1092
    • Metropolis, N.1    Rosenbluth, A.W.2    Rosenbluth, M.N.3    Teller, A.H.4    Teller, E.5
  • 45
    • 0000783674 scopus 로고
    • eds Gilks, W. R., Richardson, S. & Spiegelhalter, D. J. Chapman and Hall, New York
    • Raftery, A. in Markov Chain Monte Carlo in Practice (eds Gilks, W. R., Richardson, S. & Spiegelhalter, D. J.) 163-187 (Chapman and Hall, New York, 1995).
    • (1995) Markov Chain Monte Carlo in Practice , pp. 163-187
    • Raftery, A.1
  • 46
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Consortium, M. G. S. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
    • (2002) Nature , vol.420 , pp. 520-562
    • Consortium, M.G.S.1
  • 48
    • 0036677932 scopus 로고    scopus 로고
    • A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
    • Pupko, T., Pe'er, I., Hasegawa, M., Grauer, D. & Friedman, N. A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: application to the evolution of five gene families. Bioinformatics 18, 1116-1123 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 1116-1123
    • Pupko, T.1    Pe'er, I.2    Hasegawa, M.3    Grauer, D.4    Friedman, N.5
  • 50
    • 0036366690 scopus 로고    scopus 로고
    • eds Altman, R. B., Dunker, A. K., Hunter, L., Lauderdale, K. & Klein, T. E. Word Scientific, Singapore
    • Nielsen, R. & Huelsenbeck, J. P. in Pacific Symposium on Biocomputing (eds Altman, R. B., Dunker, A. K., Hunter, L., Lauderdale, K. & Klein, T. E.) 576-588 (Word Scientific, Singapore, 2002).
    • (2002) Pacific Symposium on Biocomputing , pp. 576-588
    • Nielsen, R.1    Huelsenbeck, J.P.2
  • 51
    • 0036272936 scopus 로고    scopus 로고
    • Accuracy and power of Bayes prediction of amino acid sites under positive selection
    • Anisimova, M., Bielawski, J. P. & Yang, Z. H. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19, 950-958 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 950-958
    • Anisimova, M.1    Bielawski, J.P.2    Yang, Z.H.3
  • 52
    • 0036803331 scopus 로고    scopus 로고
    • Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage
    • Suchard, M. A., Weiss, R. E., Dorman, K. S. & Sinsheimer, J. S. Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage. Syst. Biol. 51, 715-728 (2002).
    • (2002) Syst. Biol. , vol.51 , pp. 715-728
    • Suchard, M.A.1    Weiss, R.E.2    Dorman, K.S.3    Sinsheimer, J.S.4
  • 54
    • 0027770909 scopus 로고
    • Hantavirus pulmonary syndrome: An emerging infections disease
    • Hughes, J. M., Peters, C. J., Cohen, M. L. & Mahy, B. W. Hantavirus pulmonary syndrome: an emerging infections disease. Science 262, 850-851 (1993).
    • (1993) Science , vol.262 , pp. 850-851
    • Hughes, J.M.1    Peters, C.J.2    Cohen, M.L.3    Mahy, B.W.4
  • 55
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J. L., Kishino, H. & Felsenstein, J. Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol. 34, 3-16 (1992).
    • (1992) J. Mol. Evol. , vol.34 , pp. 3-16
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 56
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne, J. L., Kishino, H. & Felsenstein, J. An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol. 33, 114-124 (1991).
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 57
    • 0033012594 scopus 로고    scopus 로고
    • A probabilistic treatment of phylogeny and sequence alignment
    • Mitchison, G. J. A probabilistic treatment of phylogeny and sequence alignment. J. Mol. Evol. 49, 11-22 (1999).
    • (1999) J. Mol. Evol. , vol.49 , pp. 11-22
    • Mitchison, G.J.1
  • 58
    • 0034791551 scopus 로고    scopus 로고
    • Evolutionary HMMs: A Bayesian approach to multiple alignment
    • Holmes, I. & Bruno, W. J. Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 17, 803-820 (2001).
    • (2001) Bioinformatics , vol.17 , pp. 803-820
    • Holmes, I.1    Bruno, W.J.2
  • 59
    • 0035576060 scopus 로고    scopus 로고
    • Unalignable sequences and molecular evolution
    • Lee, M. S. Y. Unalignable sequences and molecular evolution. Trends Ecol. Evol. 16, 681-685 (2001).
    • (2001) Trends Ecol. Evol. , vol.16 , pp. 681-685
    • Lee, M.S.Y.1
  • 60
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • Posada, D. & Crandall, K. A. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50, 580-601 (2001).
    • (2001) Syst. Biol. , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.2
  • 61
    • 85046524655 scopus 로고    scopus 로고
    • Statistical tests of γ-distributed rate heterogeneity in models of sequence evolution in phylogenetics
    • Goldman, N. & Whelan, S. Statistical tests of γ-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol. Biol. Evol. 17, 974-978 (2000).
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 974-978
    • Goldman, N.1    Whelan, S.2
  • 62
    • 0034106726 scopus 로고    scopus 로고
    • Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters
    • Ota, R., Waddell, P. J., Hasegawa, M., Shimodaira, H. & Kishino, H. Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters. Mol. Biol. Evol. 17, 798-803 (2000).
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 798-803
    • Ota, R.1    Waddell, P.J.2    Hasegawa, M.3    Shimodaira, H.4    Kishino, H.5
  • 63
    • 0034983646 scopus 로고    scopus 로고
    • Bayesian selection of continuous-time Markov chain evolutionary models
    • Suchard, M. A., Weiss, R. E. & Sinsheimer, J. S. Bayesian selection of continuous-time Markov chain evolutionary models. Mol. Biol. Evol. 18, 1001-1013 (2001).
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1001-1013
    • Suchard, M.A.1    Weiss, R.E.2    Sinsheimer, J.S.3
  • 64
    • 0031892789 scopus 로고    scopus 로고
    • A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data
    • Lewis, P. O. A genetic algorithm for maximum-likelihood phylogeny inference using nucleotide sequence data. Mol. Biol. Evol. 15, 277-283 (1998).
    • (1998) Mol. Biol. Evol. , vol.15 , pp. 277-283
    • Lewis, P.O.1
  • 65
    • 0003035875 scopus 로고    scopus 로고
    • eds Hunter, L. & Klein, T. E. Word Scientific, London
    • Matsuda, H. in Pacific Symposium on Biocomputing (eds Hunter, L. & Klein, T. E.) 512-523 (Word Scientific, London, 1998).
    • (1998) Pacific Symposium on Biocomputing , pp. 512-523
    • Matsuda, H.1
  • 66
    • 0036679128 scopus 로고    scopus 로고
    • The metapopulation genetic algorithm: An efficient solution for the problem of large phylogeny estimation
    • Lemmon, A. R. & Milinkovitch, M. C. The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Proc. Natl Acad. Sci. USA 99, 10516-10521 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 10516-10521
    • Lemmon, A.R.1    Milinkovitch, M.C.2
  • 67
    • 0035527377 scopus 로고    scopus 로고
    • Stochastic search strategy for estimation of maximum likelihood phylogenetic trees
    • Salter, L. A. & Pearl, D. K. Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Syst. Biol. 50, 7-17 (2001).
    • (2001) Syst. Biol. , vol.50 , pp. 7-17
    • Salter, L.A.1    Pearl, D.K.2
  • 68
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • Nixon, K. C. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15, 407-414 (1999).
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.