메뉴 건너뛰기




Volumn , Issue , 2006, Pages 77-95

Taxon sampling versus computational complexity and their impact on obtaining the tree of life

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84986251481     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420009538     Document Type: Chapter
Times cited : (8)

References (52)
  • 1
    • 17744398025 scopus 로고    scopus 로고
    • More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
    • Rokas, A. and Carroll, S.B., More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy, Mol. Biol. Evol., 22, 1337, 2005.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1337
    • Rokas, A.1    Carroll, S.B.2
  • 2
    • 19944417239 scopus 로고    scopus 로고
    • Supertree construction in the genomic age, in Molecular Evolution: Producing the Biochemical Data
    • part B, Zimmer, E.A. and Roalson, E., Eds., Elsevier, Amsterdam
    • Bininda-Emonds, O.R.P., Supertree construction in the genomic age, in Molecular Evolution: Producing the Biochemical Data, part B, Zimmer, E.A. and Roalson, E., Eds., Methods in Enzymology, Vol. 395, Elsevier, Amsterdam, 2005, 745.
    • (2005) Methods in Enzymology , vol.395 , pp. 745
    • Bininda-Emonds, O.R.P.1
  • 3
    • 0042695888 scopus 로고    scopus 로고
    • The challenge of constructing large phylogenetic trees
    • Sanderson, M.J. and Driskell, A.C., The challenge of constructing large phylogenetic trees, Trends Pl. Sci., 8, 374, 2003.
    • (2003) Trends Pl. Sci. , vol.8 , pp. 374
    • Sanderson, M.J.1    Driskell, A.C.2
  • 4
    • 11144357823 scopus 로고    scopus 로고
    • Taxonomy as a fundamental discipline
    • Wilson, E.O., Taxonomy as a fundamental discipline, Philos. Trans. R. Soc. Lond. B, 359, 739, 2004.
    • (2004) Philos. Trans. R. Soc. Lond. B , vol.359 , pp. 739
    • Wilson, E.O.1
  • 5
    • 84959792503 scopus 로고
    • The number of evolutionary trees
    • Felsenstein, J., The number of evolutionary trees, Syst. Zool., 27, 27, 1978.
    • (1978) Syst. Zool. , vol.27 , pp. 27
    • Felsenstein, J.1
  • 6
    • 10244219919 scopus 로고    scopus 로고
    • QuickJoin: Fast neighbour-joining tree reconstruction
    • Mailund, T. and Pedersen, C.N., QuickJoin: fast neighbour-joining tree reconstruction, Bioinformatics, 20, 3261, 2004.
    • (2004) Bioinformatics , vol.20 , pp. 3261
    • Mailund, T.1    Pedersen, C.N.2
  • 9
    • 14044251530 scopus 로고    scopus 로고
    • Rec-I-DCM3: A fast algorithmic technique for reconstructing large phylogenetic trees
    • IEEE Computer Society Press, Stanford, California
    • Roshan, U. et al., Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees, in Proceedings of the IEEE Computational Systems Bioinformatics conference (CSB), IEEE Computer Society Press, Stanford, California, 2004.
    • (2004) Proceedings of the IEEE Computational Systems Bioinformatics conference (CSB)
    • Roshan, U.1
  • 11
    • 19044382857 scopus 로고    scopus 로고
    • Towards building the tree of life: A simulation study for all angiosperm taxa
    • Salamin, N., Hodkinson, T.R., and Savolainen, V., Towards building the tree of life: a simulation study for all angiosperm taxa, Syst. Biol., 54, 183, 2005.
    • (2005) Syst. Biol. , vol.54 , pp. 183
    • Salamin, N.1    Hodkinson, T.R.2    Savolainen, V.3
  • 12
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • Hillis, D.M., Inferring complex phylogenies, Nature, 383, 130, 1996.
    • (1996) Nature , vol.383 , pp. 130
    • Hillis, D.M.1
  • 13
    • 0035222013 scopus 로고    scopus 로고
    • Scaling of accuracy in extremely large phylogenetic trees
    • Altman, R.B. et al., Eds., World Scientific Publishing Company, River Edge, NJ
    • Bininda-Emonds, O.R.P. et al., Scaling of accuracy in extremely large phylogenetic trees, in Pacific Symposium on Biocomputing 2001, Altman, R.B. et al., Eds., World Scientific Publishing Company, River Edge, NJ, 2000, 547.
    • (2000) Pacific Symposium on Biocomputing 2001 , pp. 547
    • Bininda-Emonds, O.R.P.1
  • 14
    • 0033480324 scopus 로고    scopus 로고
    • A few logs suffice to build (almost) all trees (I)
    • Erdös, P.L. et al., A few logs suffice to build (almost) all trees (I), Random Struc. Alg., 14, 153, 1999.
    • (1999) Random Struc. Alg. , vol.14 , pp. 153
    • Erdös, P.L.1
  • 15
    • 0001860411 scopus 로고    scopus 로고
    • A few logs suffice to build (almost) all trees: Part II
    • Erdös, P.L. et al., A few logs suffice to build (almost) all trees: part II, Theoret. Comput. Sci., 221, 77, 1999.
    • (1999) Theoret. Comput. Sci. , vol.221 , pp. 77
    • Erdös, P.L.1
  • 16
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • Huelsenbeck, J.P. and Hillis, D.M., Success of phylogenetic methods in the four-taxon case, Syst. Biol., 42, 247, 1993.
    • (1993) Syst. Biol. , vol.42 , pp. 247
    • Huelsenbeck, J.P.1    Hillis, D.M.2
  • 17
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten, J., A review of long-branch attraction, Cladistics, 21, 163, 2005.
    • (2005) Cladistics , vol.21 , pp. 163
    • Bergsten, J.1
  • 18
    • 0032023889 scopus 로고    scopus 로고
    • Taxonomic sampling, phylogenetic accuracy, and investigator bias
    • Hillis, D.M., Taxonomic sampling, phylogenetic accuracy, and investigator bias, Syst. Biol., 47, 3, 1998.
    • (1998) Syst. Biol. , vol.47 , pp. 3
    • Hillis, D.M.1
  • 19
    • 0036699885 scopus 로고    scopus 로고
    • Increased taxon sampling is advantageous for phylogenetic inference
    • Pollock, D.D. et al., Increased taxon sampling is advantageous for phylogenetic inference, Syst. Biol., 51, 664, 2002.
    • (2002) Syst. Biol. , vol.51 , pp. 664
    • Pollock, D.D.1
  • 20
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal, A., Is it better to add taxa or characters to a difficult phylogenetic problem? Syst. Biol., 47, 9, 1998.
    • (1998) Syst. Biol. , vol.47 , pp. 9
    • Graybeal, A.1
  • 21
    • 0035845536 scopus 로고    scopus 로고
    • Incomplete taxon sampling is not a problem for phylogenetic inference
    • Rosenberg, M.S. and Kumar, S., Incomplete taxon sampling is not a problem for phylogenetic inference, Proc. Natl. Acad. Sci. USA, 98, 10751, 2001.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 10751
    • Rosenberg, M.S.1    Kumar, S.2
  • 22
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • Strimmer, K. and von Haeseler, A., Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies, Mol. Biol. Evol., 13, 964, 1996.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964
    • Strimmer, K.1    von Haeseler, A.2
  • 23
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson, D.H., Nettles, S.M., and Warnow, T.J., Disk-covering, a fast-converging method for phylogenetic tree reconstruction, J. Comput. Biol., 6, 369, 1999.
    • (1999) J. Comput. Biol. , vol.6 , pp. 369
    • Huson, D.H.1    Nettles, S.M.2    Warnow, T.J.3
  • 25
    • 0037314098 scopus 로고    scopus 로고
    • Inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson, M.J., r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, 19, 301, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 301
    • Sanderson, M.J.1
  • 26
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A. and Grassly, N.C., Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Appl. Biosci., 13, 235, 1997.
    • (1997) Comput. Appl. Biosci. , vol.13 , pp. 235
    • Rambaut, A.1    Grassly, N.C.2
  • 27
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis, D.M., Moritz, C., and Mable, B.K., Eds., Sinauer Associates, Sunderland, Massachusetts
    • Swofford, D.L. et al., Phylogenetic inference, in Molecular Systematics, Hillis, D.M., Moritz, C., and Mable, B.K., Eds., Sinauer Associates, Sunderland, Massachusetts, 1996, 407.
    • (1996) Molecular Systematics , pp. 407
    • Swofford, D.L.1
  • 28
    • 2442489795 scopus 로고    scopus 로고
    • Performance of supertree methods on various data set decompositions
    • Bininda-Emonds, O.R.P., Ed., Kluwer Academic, Dordrecht, Netherlands
    • Roshan, U. et al., Performance of supertree methods on various data set decompositions, in Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Bininda-Emonds, O.R.P., Ed., Kluwer Academic, Dordrecht, Netherlands, 2004, 301.
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life , pp. 301
    • Roshan, U.1
  • 31
    • 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, 1999.
    • (1999) Cladistics , vol.15 , pp. 407
    • Nixon, K.C.1
  • 32
    • 0036857358 scopus 로고    scopus 로고
    • Bateman, A., and Durbin, R., QuickTree: Building huge neighbour-joining trees of protein sequences
    • Howe, K., Bateman, A., and Durbin, R., QuickTree: building huge neighbour-joining trees of protein sequences, Bioinformatics, 18, 1546, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 1546
    • Howe, K.1
  • 33
    • 14644397888 scopus 로고    scopus 로고
    • RAxML-III: A fast program for maximum likelihood-based inference of large phylogenetic trees
    • Stamatakis, A., Ludwig, T., and Meier, H., RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees, Bioinformatics, 21, 456, 2005.
    • (2005) Bioinformatics , vol.21 , pp. 456
    • Stamatakis, A.1    Ludwig, T.2    Meier, H.3
  • 34
    • 18244389982 scopus 로고    scopus 로고
    • AxML: A fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method
    • Stamatakis, A.P. et al., AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood method, Proc. IEEE Comput. Soc. Bioinform. Conf., 1, 21, 2002.
    • (2002) Proc. IEEE Comput. Soc. Bioinform. Conf. , vol.1 , pp. 21
    • Stamatakis, A.P.1
  • 35
    • 84959758123 scopus 로고
    • Congruence between morphometric and allozyme data for Menidia species: A reappraisal
    • Colless, D.H., Congruence between morphometric and allozyme data for Menidia species: a reappraisal, Syst. Zool., 29, 288, 1980.
    • (1980) Syst. Zool. , vol.29 , pp. 288
    • Colless, D.H.1
  • 36
    • 0005745748 scopus 로고
    • Predictivity and stability in classifications: Some comments on recent studies
    • Colless, D.H., Predictivity and stability in classifications: some comments on recent studies, Syst. Zool., 30, 325, 1981.
    • (1981) Syst. Zool. , vol.30 , pp. 325
    • Colless, D.H.1
  • 37
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson, D.F. and Foulds, L.R., Comparison of phylogenetic trees, Math. Biosci., 53, 131, 1981.
    • (1981) Math. Biosci. , vol.53 , pp. 131
    • Robinson, D.F.1    Foulds, L.R.2
  • 38
    • 52449147252 scopus 로고
    • The complexity of reconstructing trees from qualitative characters and subtrees
    • Steel, M., The complexity of reconstructing trees from qualitative characters and subtrees, J. Classif., 9, 91, 1992.
    • (1992) J. Classif. , vol.9 , pp. 91
    • Steel, M.1
  • 39
    • 0242365676 scopus 로고    scopus 로고
    • Genome-scale approaches to resolving incongruence in molecular phylogenies
    • Rokas, A. et al., Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 2003.
    • (2003) Nature , vol.425 , pp. 798
    • Rokas, A.1
  • 40
    • 0028362880 scopus 로고
    • Application and accuracy of molecular phylogenies
    • Hillis, D.M., Huelsenbeck, J.P., and Cunningham, C.W., Application and accuracy of molecular phylogenies, Science, 264, 671, 1994.
    • (1994) Science , vol.264 , pp. 671
    • Hillis, D.M.1    Huelsenbeck, J.P.2    Cunningham, C.W.3
  • 41
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon, S. and Gascuel, O., A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 2003.
    • (2003) Syst. Biol. , vol.52 , pp. 696
    • Guindon, S.1    Gascuel, O.2
  • 42
    • 0032766033 scopus 로고    scopus 로고
    • Multiple local maxima for likelihoods of phylogenetic trees: A simulation study
    • Rogers, J.S. and Swofford, D.L., Multiple local maxima for likelihoods of phylogenetic trees: a simulation study, Mol. Biol. Evol., 16, 1079, 1999.
    • (1999) Mol. Biol. Evol. , vol.16 , pp. 1079
    • Rogers, J.S.1    Swofford, D.L.2
  • 43
    • 0033499153 scopus 로고    scopus 로고
    • Analyzing large data sets in reasonable times: Solutions for composite optima
    • Goloboff, P.A., Analyzing large data sets in reasonable times: solutions for composite optima, Cladistics, 15, 415, 1999.
    • (1999) Cladistics , vol.15 , pp. 415
    • Goloboff, P.A.1
  • 44
    • 0038781911 scopus 로고    scopus 로고
    • Assessing internal support with large phylogenetic DNA matrices
    • Salamin, N. et al., Assessing internal support with large phylogenetic DNA matrices, Mol. Phylogenet. Evol., 27, 528, 2003.
    • (2003) Mol. Phylogenet. Evol. , vol.27 , pp. 528
    • Salamin, N.1
  • 45
    • 0028069573 scopus 로고
    • Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree
    • Hasegawa, M. and Kishino, H., Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree, Mol. Biol. Evol., 11, 142, 1994.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 142
    • Hasegawa, M.1    Kishino, H.2
  • 46
    • 0025181359 scopus 로고
    • Maximum likelihood inference of protein phylogeny and the origin of chloroplasts
    • Kishino, H., Miyata, T., and Hasegawa, M., Maximum likelihood inference of protein phylogeny and the origin of chloroplasts, J. Mol. Evol., 31, 151, 1990.
    • (1990) J. Mol. Evol. , vol.31 , pp. 151
    • Kishino, H.1    Miyata, T.2    Hasegawa, M.3
  • 47
    • 0142089657 scopus 로고    scopus 로고
    • Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data
    • Lathrop, R. et al., Eds., Universal Academy Press, Tokyo
    • Waddell, P.J., Kishino, H., and Ota, R., Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data, in Genome Informatics 2002, Lathrop, R. et al., Eds., Universal Academy Press, Tokyo, 2002, 82.
    • (2002) Genome Informatics 2002 , pp. 82
    • Waddell, P.J.1    Kishino, H.2    Ota, R.3
  • 48
    • 0030315308 scopus 로고    scopus 로고
    • General inconsistency conditions for maximum parsimony: Effects of branch lengths and increasing numbers of taxa
    • Kim, J., General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa, Syst. Biol., 45, 363, 1996.
    • (1996) Syst. Biol. , vol.45 , pp. 363
    • Kim, J.1
  • 49
    • 3242801484 scopus 로고    scopus 로고
    • IQPNNI: Moving fast through tree space and stopping in time
    • le Vinh, S. and Von Haeseler, A., IQPNNI: moving fast through tree space and stopping in time, Mol. Biol. Evol., 21, 1565, 2004.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1565
    • Le Vinh, S.1    Von Haeseler, A.2
  • 51
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony supertree construction
    • Bininda-Emonds, O.R.P. and Sanderson, M.J., Assessment of the accuracy of matrix representation with parsimony supertree construction, Syst. Biol., 50, 565, 2001.
    • (2001) Syst. Biol. , vol.50 , pp. 565
    • Bininda-Emonds, O.R.P.1    Sanderson, M.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.