메뉴 건너뛰기




Volumn 56, Issue 4, 2007, Pages 578-590

Summarizing a posterior distribution of trees using agreement subtrees

Author keywords

Agreement subtrees; Bayesian phylogenetic inference; Credible sets; Posterior distribution of trees; Threshold accepting

Indexed keywords

ALGORITHM; ARTICLE; BAYES THEOREM; BIOLOGICAL MODEL; COMPUTER SIMULATION; PHYLOGENY;

EID: 34547482037     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150701485091     Document Type: Article
Times cited : (29)

References (35)
  • 1
    • 0000388213 scopus 로고
    • On the convergence of Threshold Accepting
    • Althofer, I., and K.-U. Koschnick. 1991. On the convergence of Threshold Accepting. Appl. Math. Optim. 24:183-195.
    • (1991) Appl. Math. Optim , vol.24 , pp. 183-195
    • Althofer, I.1    Koschnick, K.-U.2
  • 2
    • 0006683426 scopus 로고    scopus 로고
    • Maximum agreement subtree in a set of evolutionary trees: Metrics and effdent algorithms
    • Amir, A., and D. Keselman. 1997. Maximum agreement subtree in a set of evolutionary trees: Metrics and effdent algorithms. SIAM J. Comput. 26:1656-1669.
    • (1997) SIAM J. Comput , vol.26 , pp. 1656-1669
    • Amir, A.1    Keselman, D.2
  • 5
    • 0035189546 scopus 로고    scopus 로고
    • An O(n log n) algorithm for the maximum agreement subtree problem for binary trees
    • Cole, R., M. Farach-Colton, R. Hariharans, T. Przytycka, and M. Thorup. 2000. An O(n log n) algorithm for the maximum agreement subtree problem for binary trees. SIAM J. Comput. 30:1385-1404.
    • (2000) SIAM J. Comput , vol.30 , pp. 1385-1404
    • Cole, R.1    Farach-Colton, M.2    Hariharans, R.3    Przytycka, T.4    Thorup, M.5
  • 6
    • 25144482720 scopus 로고
    • Threshold accepting: A general purpose optimization algorithm
    • Dueck, G., and T. Scheuer. 1990. Threshold accepting: A general purpose optimization algorithm. J. Comput. Phys. 90:161-175.
    • (1990) J. Comput. Phys , vol.90 , pp. 161-175
    • Dueck, G.1    Scheuer, T.2
  • 7
    • 0000399236 scopus 로고
    • Obtaining common pruned trees
    • Finden, C. R., and A. D. Gordon. 1985. Obtaining common pruned trees. J. Classif. 2:255-276.
    • (1985) J. Classif , vol.2 , pp. 255-276
    • Finden, C.R.1    Gordon, A.D.2
  • 8
    • 33748204460 scopus 로고    scopus 로고
    • Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and super-matrix analyses of multiple gene data sets
    • Fulton, T. L., and C. Strobeck. 2006. Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and super-matrix analyses of multiple gene data sets. Mol. Phylogenet. Evol. 41:165-181.
    • (2006) Mol. Phylogenet. Evol , vol.41 , pp. 165-181
    • Fulton, T.L.1    Strobeck, C.2
  • 10
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Greybeal, A. 1998. Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol. 47:9-17.
    • (1998) Syst. Biol , vol.47 , pp. 9-17
    • Greybeal, A.1
  • 11
    • 0035047175 scopus 로고    scopus 로고
    • Spedation, hybrid zones and phylogeography - Or seeing genes in space and time
    • Hewitt, G. M. 2001. Spedation, hybrid zones and phylogeography - Or seeing genes in space and time. Mol. Ecol. 10:537-549.
    • (2001) Mol. Ecol , vol.10 , pp. 537-549
    • Hewitt, G.M.1
  • 12
    • 0242669921 scopus 로고    scopus 로고
    • Is sparse taxon sampling a problem for phylogenetic inference?
    • Hillis, D. M., D. D. Pollock, J. A. McGuire, and D. J. Zwickl. 2003. Is sparse taxon sampling a problem for phylogenetic inference? Syst. Biol. 52:124-126.
    • (2003) Syst. Biol , vol.52 , pp. 124-126
    • Hillis, D.M.1    Pollock, D.D.2    McGuire, J.A.3    Zwickl, D.J.4
  • 13
    • 0034849408 scopus 로고    scopus 로고
    • MrBayes: Bayesian inference of phylogenetic trees
    • Huelsenbeck, J. P. and F. Ronquist. 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
  • 14
    • 30744470609 scopus 로고    scopus 로고
    • Application of phylogenetic networks in evolutionary studies
    • Huson, D., and D. Bryant. 2006. Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol. 23:254-267.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 254-267
    • Huson, D.1    Bryant, D.2
  • 15
    • 3142748715 scopus 로고    scopus 로고
    • Global optimization performance measures for generalized hill climbing algorithms
    • Jacobson, S. H., and E. Yucesan. 2004. Global optimization performance measures for generalized hill climbing algorithms. J. Global Optim. 29:173-190.
    • (2004) J. Global Optim , vol.29 , pp. 173-190
    • Jacobson, S.H.1    Yucesan, E.2
  • 16
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • Kirkpatrick, S., C. D. Gelatt, and M. P. Vecchi. 1983. Optimization by simulated annealing. Science 220:671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 17
    • 0036900040 scopus 로고    scopus 로고
    • Statistical phylogeography
    • Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635.
    • (2002) Mol. Ecol , vol.11 , pp. 2623-2635
    • Knowles, L.L.1    Maddison, W.P.2
  • 19
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock, D. D., D. J. Zwickl, J. A. McGuire, and D. M. Hillis. 2002. Increased taxon sampling is advantageous for phylogenetic inference. Syst. Biol. 51:664-671.
    • (2002) Syst. Biol , vol.51 , pp. 664-671
    • Pollock, D.D.1    Zwickl, D.J.2    McGuire, J.A.3    Hillis, D.M.4
  • 20
    • 0032225752 scopus 로고    scopus 로고
    • Taxon sampling and the accuracy of large phylogenies
    • Rannala, B., J. P. Huelsenbeck, Z. Yang, and R. Nielsen. 1998. Taxon sampling and the accuracy of large phylogenies. Syst. Biol. 47:702-710.
    • (1998) Syst. Biol , vol.47 , pp. 702-710
    • Rannala, B.1    Huelsenbeck, J.P.2    Yang, Z.3    Nielsen, R.4
  • 21
    • 0030749810 scopus 로고    scopus 로고
    • Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method
    • Rannala, B., and Z. Yang. 1997. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Mol. Biol. Evol. 14:717-724.
    • (1997) Mol. Biol. Evol , vol.14 , pp. 717-724
    • Rannala, B.1    Yang, Z.2
  • 22
    • 0041386108 scopus 로고    scopus 로고
    • MrBayes 3: Bayesian phylogenetic inference under mixed models
    • Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2003) Bioinformatics , vol.19 , pp. 1572-1574
    • Ronquist, F.1    Huelsenbeck, J.P.2
  • 23
    • 0035845536 scopus 로고    scopus 로고
    • Incomplete taxon sampling is not a problem for phylogenetic inference
    • Rosenberg, M., and S. Kumar. 2001. Incomplete taxon sampling is not a problem for phylogenetic inference. Proc. Natl. Acad. Sci. USA 98:10751-10756.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10751-10756
    • Rosenberg, M.1    Kumar, S.2
  • 24
    • 0037291976 scopus 로고    scopus 로고
    • Taxon sampling, bioinformatics, and phylogenomics
    • Rosenberg, M., and S. Kumar. 2003. Taxon sampling, bioinformatics, and phylogenomics. Syst. Biol. 52:119-124.
    • (2003) Syst. Biol , vol.52 , pp. 119-124
    • Rosenberg, M.1    Kumar, S.2
  • 25
    • 0036135468 scopus 로고    scopus 로고
    • Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach
    • Sanderson, M. J. 2002. Estimating absolute rates of molecular evolution and divergence times: A penalized likelihood approach. Mol. Biol. Evol. 19:101-109.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 101-109
    • Sanderson, M.J.1
  • 26
    • 0036926048 scopus 로고    scopus 로고
    • Troubleshooting molecular phylogenetic analysis
    • Sanderson, M. J., and H. B. Schaffer. 2002. Troubleshooting molecular phylogenetic analysis. Ann. Rev. Ecol. Syst. 33:49-72.
    • (2002) Ann. Rev. Ecol. Syst , vol.33 , pp. 49-72
    • Sanderson, M.J.1    Schaffer, H.B.2
  • 28
    • 0031741182 scopus 로고    scopus 로고
    • Estimating the rate of evolution of the rate of molecular evolution
    • Thorne, J. L., H. Kishino, and I. S. Painter. 1998. Estimating the rate of evolution of the rate of molecular evolution. Mol. Biol. Evol. 15:1647-57.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 1647-1657
    • Thorne, J.L.1    Kishino, H.2    Painter, I.S.3
  • 29
    • 12044253960 scopus 로고
    • Common cladistic information and its consensus representation: Reduced Adams and reduced cladistic consensus trees and profiles
    • Wilkinson, M. 1994. Common cladistic information and its consensus representation: Reduced Adams and reduced cladistic consensus trees and profiles. Syst. Biol. 43:343-368.
    • (1994) Syst. Biol , vol.43 , pp. 343-368
    • Wilkinson, M.1
  • 30
    • 0030038509 scopus 로고    scopus 로고
    • Majority-rule reduced consensus trees and their use in bootstrapping
    • Wilkinson, M. 1996. Majority-rule reduced consensus trees and their use in bootstrapping. Mol. Biol. Evol. 13:437-444.
    • (1996) Mol. Biol. Evol , vol.13 , pp. 437-444
    • Wilkinson, M.1
  • 31
    • 0034351401 scopus 로고    scopus 로고
    • A chain is no stronger than it s weakest link: Double decay analysis of phylogenetic hypotheses
    • Wilkinson, M., J. L. Thorley, and P. Upchurch. 2000. A chain is no stronger than it s weakest link: Double decay analysis of phylogenetic hypotheses. Syst. Biol. 49:754-776.
    • (2000) Syst. Biol , vol.49 , pp. 754-776
    • Wilkinson, M.1    Thorley, J.L.2    Upchurch, P.3
  • 32
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 33
    • 0029469716 scopus 로고
    • Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem
    • Yang, Z., N. Goldman, and A. E. Friday. 1995. Maximum likelihood trees from DNA sequences: A peculiar statistical estimation problem. Syst. Biol. 44:384-399.
    • (1995) Syst. Biol , vol.44 , pp. 384-399
    • Yang, Z.1    Goldman, N.2    Friday, A.E.3
  • 34
    • 16344378246 scopus 로고    scopus 로고
    • Bayes empirical Bayes inference of amino acid sites under positive selection
    • Yang, Z., W. S. W. Wong, and R. Nielsen. 2005. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol. Biol. Evol. 22:1107-1118.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1107-1118
    • Yang, Z.1    Wong, W.S.W.2    Nielsen, R.3
  • 35
    • 0036699481 scopus 로고    scopus 로고
    • Increased taxon sampling greatly reduces phylogenetic error
    • Zwickl, D., and D. Hillis. 2002. Increased taxon sampling greatly reduces phylogenetic error. Syst. Biol. 51:588-598.
    • (2002) Syst. Biol , vol.51 , pp. 588-598
    • Zwickl, D.1    Hillis, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.