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Volumn 54, Issue 3, 2005, Pages 471-482

Analysis and visualization of tree space

Author keywords

Bayesian analysis; Multidimensional scaling; Phylogenetic analysis; Tree space; Visualization

Indexed keywords

ARTICLE; BAYES THEOREM; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER PROGRAM; METHODOLOGY; PHYLOGENY; STATISTICAL ANALYSIS;

EID: 22844442543     PISSN: 10635157     EISSN: None     Source Type: Journal    
DOI: 10.1080/10635150590946961     Document Type: Article
Times cited : (170)

References (42)
  • 1
    • 0037329391 scopus 로고    scopus 로고
    • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence
    • Alfaro, M. E., S. Zoller, and F. Lutzoni. 2003. Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence. Mol. Biol. Evol. 20:255-266.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 255-266
    • Alfaro, M.E.1    Zoller, S.2    Lutzoni, F.3
  • 4
    • 0036005521 scopus 로고    scopus 로고
    • Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera
    • Buckley, T. R., P. Arensburger, C. Simon, and G. K. Chambers. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18.
    • (2002) Syst. Biol. , vol.51 , pp. 4-18
    • Buckley, T.R.1    Arensburger, P.2    Simon, C.3    Chambers, G.K.4
  • 5
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • F. R. Hodson, D. G. Kendall, and P. Tautu, eds. Edinburgh University Press, Edinburgh
    • Buneman, P. 1971. The recovery of trees from measures of dissimilarity. Pages 387-395 in Mathematics in archaeological and historical sciences. (F. R. Hodson, D. G. Kendall, and P. Tautu, eds.). Edinburgh University Press, Edinburgh.
    • (1971) Mathematics in Archaeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 6
    • 0042069655 scopus 로고    scopus 로고
    • Comparing bootstrap and posterior probability values in the four-taxon case
    • Cummings, M. P., S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. 55:477-487.
    • (2003) Syst. Biol. , vol.55 , pp. 477-487
    • Cummings, M.P.1    Handley, S.A.2    Myers, D.S.3    Reed, D.L.4    Rokas, A.5    Winka, K.6
  • 7
    • 0003002776 scopus 로고
    • Optimal algorithms for comparing trees with labeled leaves
    • Day, W. H. E. 1985. Optimal algorithms for comparing trees with labeled leaves. J. Classification 2:7-28.
    • (1985) J. Classification , vol.2 , pp. 7-28
    • Day, W.H.E.1
  • 8
    • 0030581603 scopus 로고    scopus 로고
    • Bootstrap confidence levels for phylogenetic trees
    • Efron, B., E. Halloran, and S. Holmes. 1996. Bootstrap confidence levels for phylogenetic trees. Proc. Natl. Acad. Sci. USA 93:7085-7090.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 7085-7090
    • Efron, B.1    Halloran, E.2    Holmes, S.3
  • 9
    • 0242487486 scopus 로고    scopus 로고
    • Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics
    • Erixon, P., B. Svennblad, T. Britton, and B. Oxelman. 2003. Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics. Syst. Biol. 52:665-673.
    • (2003) Syst. Biol. , vol.52 , pp. 665-673
    • Erixon, P.1    Svennblad, B.2    Britton, T.3    Oxelman, B.4
  • 10
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 12
    • 0002388372 scopus 로고    scopus 로고
    • Strategies for improving MCMC
    • W. R. Gilks, G.O. Roberts, and D. J. Spiegelhalter, eds. Chapman and Hall, London
    • Gilks, W. R., and G. O. Roberts. 1996. Strategies for improving MCMC Pages 89-114 in Markov Monte Carlo in practice (W. R. Gilks, G.O. Roberts, and D. J. Spiegelhalter, eds). Chapman and Hall, London.
    • (1996) Markov Monte Carlo in Practice , pp. 89-114
    • Gilks, W.R.1    Roberts, G.O.2
  • 13
    • 12044253190 scopus 로고
    • An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis
    • Hillis, D. M., and J. J. Bull. 1993. An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42:182-192.
    • (1993) Syst. Biol. , vol.42 , pp. 182-192
    • Hillis, D.M.1    Bull, J.J.2
  • 14
    • 11144319958 scopus 로고    scopus 로고
    • Phylogeny of the New World true frogs (Rana)
    • Hillis, D. M., and T. P. Wilcox. 2005. Phylogeny of the New World true frogs (Rana). Mol. Phylogenet. Evol. 34:299-314.
    • (2005) Mol. Phylogenet. Evol. , vol.34 , pp. 299-314
    • Hillis, D.M.1    Wilcox, T.P.2
  • 15
    • 11144277878 scopus 로고    scopus 로고
    • Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models
    • Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-913.
    • (2004) Syst. Biol. , vol.53 , pp. 904-913
    • Huelsenbeck, J.P.1    Rannala, B.2
  • 16
    • 0041386108 scopus 로고    scopus 로고
    • MRBAYES: Bayesian phylogenetic inference under mixed models
    • Huelsenbeck, J. P., and F. Ronquist. 2001. MRBAYES: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
    • (2001) Bioinformatics , vol.19 , pp. 1572-1574
    • Huelsenbeck, J.P.1    Ronquist, F.2
  • 17
    • 0035861456 scopus 로고    scopus 로고
    • Bayesian inference of phylogeny and its impact on evolutionary biology
    • Huelsenbeck, J. P., F. Ronquist, R. Nielson, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314.
    • (2001) Science , vol.294 , pp. 2310-2314
    • Huelsenbeck, J.P.1    Ronquist, F.2    Nielson, R.3    Bollback, J.P.4
  • 18
    • 0032976397 scopus 로고    scopus 로고
    • Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees
    • Larget, B., and D. L. Simon. 1999. Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16:750-759.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 750-759
    • Larget, B.1    Simon, D.L.2
  • 19
    • 12044252747 scopus 로고
    • What is the bootstrap technique?
    • Li, W.-H., and A. Zharkikh. 1994. What is the bootstrap technique? Syst. Biol. 43:424-430.
    • (1994) Syst. Biol. , vol.43 , pp. 424-430
    • Li, W.-H.1    Zharkikh, A.2
  • 21
    • 84960569058 scopus 로고
    • The discovery and importance of multiple islands of most-parsimonious trees
    • Maddison, D. R. 1991. The discovery and importance of multiple islands of most-parsimonious trees. Syst. Zool. 40:315-328.
    • (1991) Syst. Zool. , vol.40 , pp. 315-328
    • Maddison, D.R.1
  • 26
    • 0002393841 scopus 로고
    • The use of tree comparison metrics
    • Penny, D., and M. D. Hendy. 1985. The use of tree comparison metrics. Syst. Zool. 34:75-82.
    • (1985) Syst. Zool. , vol.34 , pp. 75-82
    • Penny, D.1    Hendy, M.D.2
  • 27
    • 0035527410 scopus 로고    scopus 로고
    • Selecting the best-fit model of nucleotide substitution
    • Posada, D., and K. A. Crandall. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50:580-601.
    • (2001) Syst. Biol. , vol.50 , pp. 580-601
    • Posada, D.1    Crandall, K.A.2
  • 28
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., and N. C. Grassly. 1997. Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 13:235-238.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 29
    • 0039348203 scopus 로고
    • Comparison of weighted labeled trees
    • Robinson, D. F., and L. R. Foulds, 1979. Comparison of weighted labeled trees. Lect. Notes Math. 748:119-126.
    • (1979) Lect. Notes Math. , vol.748 , pp. 119-126
    • Robinson, D.F.1    Foulds, L.R.2
  • 30
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D. F., and L. R. Foulds. 1981. Comparison of phylogenetic trees. Math. Biosci. 53:131-147.
    • (1981) Math. Biosci. , vol.53 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 31
    • 0027237771 scopus 로고
    • Calibrating the bootstrap test of monophyly
    • Rodrigo, A. G. 1993. Calibrating the bootstrap test of monophyly. Int. J. Parasitol. 23:507-514.
    • (1993) Int. J. Parasitol. , vol.23 , pp. 507-514
    • Rodrigo, A.G.1
  • 32
    • 11244353178 scopus 로고    scopus 로고
    • Statistically based postprocessing of phylogenetic analysis by clustering
    • Stockham, C., L.-S. Wang, and T. Warnow. 2002. Statistically based postprocessing of phylogenetic analysis by clustering. Bioinformatics 18:5285-5293.
    • (2002) Bioinformatics , vol.18 , pp. 5285-5293
    • Stockham, C.1    Wang, L.-S.2    Warnow, T.3
  • 33
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y., G. V. Glazko, and M. Nei. 2002. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99:16138-16143.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 34
    • 0002529938 scopus 로고
    • When are phylogeny estimates from molecular and morphological data incongruent?
    • M. M. Miyamoto and J. Cracraft, eds. Oxford University Press, New York
    • Swofford, D. L. 1991. When are phylogeny estimates from molecular and morphological data incongruent? Pages 295-333 in Phylogenetic analysis of DNA aequences (M. M. Miyamoto and J. Cracraft, eds.). Oxford University Press, New York.
    • (1991) Phylogenetic Analysis of DNA Aequences , pp. 295-333
    • Swofford, D.L.1
  • 36
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • D. M. Hillis, C. Moritz, and B. K. Mable, eds. Sinauer Associates, Sunderland, Massachusetts
    • Swofford, D. L., G. J. Olsen, P. J. Waddell, and D. M. Hillis. 1996. Phylogenetic inference. Pages 407-514 in Molecular systematics, 2nd edition (D. M. Hillis, C. Moritz, and B. K. Mable, eds.). Sinauer Associates, Sunderland, Massachusetts.
    • (1996) Molecular Systematics, 2nd Edition , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 37
    • 0036368188 scopus 로고    scopus 로고
    • Phylogeny of the tree swallow genus Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences
    • Whittingham, L. A., B. Slikas, D. W. Winkler, and F. H. Sheldon. 2002. Phylogeny of the tree swallow genus Tachycineta (Aves: Hirundinidae), by Bayesian analysis of mitochondrial DNA sequences. Mol. Phylogenet. Evol. 22:430-441.
    • (2002) Mol. Phylogenet. Evol. , vol.22 , pp. 430-441
    • Whittingham, L.A.1    Slikas, B.2    Winkler, D.W.3    Sheldon, F.H.4
  • 38
    • 0036431235 scopus 로고    scopus 로고
    • Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support
    • Wilcox, T. P., D. J. Zwickl, T. A. Heath, and D. M. Hillis. 2002. Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Mol. Phylogenet. Evol. 25:361-371.
    • (2002) Mol. Phylogenet. Evol. , vol.25 , pp. 361-371
    • Wilcox, T.P.1    Zwickl, D.J.2    Heath, T.A.3    Hillis, D.M.4
  • 40
    • 0026443498 scopus 로고
    • Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock
    • Zharkikh, A., and W.-H. Li. 1992a. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol. Biol. Evol. 9:1119-1147.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 1119-1147
    • Zharkikh, A.1    Li, W.-H.2
  • 41
    • 0026484750 scopus 로고
    • Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock
    • Zharkikh, A., and W.-H. Li. 1992b. Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. II. Four taxa without a molecular clock. J. Mol. Evol. 35:356-366.
    • (1992) J. Mol. Evol. , vol.35 , pp. 356-366
    • Zharkikh, A.1    Li, W.-H.2
  • 42
    • 0029261787 scopus 로고
    • Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique
    • Zharkikh, A., and W.-H. Li. 1995. Estimation of confidence in phylogeny: The complete-and-partial bootstrap technique. Mol. Phylogenet. Evol. 4:44-63.
    • (1995) Mol. Phylogenet. Evol. , vol.4 , pp. 44-63
    • Zharkikh, A.1    Li, W.-H.2


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