메뉴 건너뛰기




Volumn 26, Issue 12, 2010, Pages

SUPERTRIPLETS: A triplet-based supertree approach to phylogenomics

Author keywords

[No Author keywords available]

Indexed keywords

MAMMALIA;

EID: 77954209722     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq196     Document Type: Article
Times cited : (53)

References (65)
  • 1
    • 84959774562 scopus 로고
    • Consensus techniques and the comparison of taxonomic trees
    • Adams,E.N. (1972) Consensus techniques and the comparison of taxonomic trees. Syst. Zool., 21, 390-397.
    • (1972) Syst. Zool. , vol.21 , pp. 390-397
    • Adams, E.N.1
  • 2
    • 43049099668 scopus 로고    scopus 로고
    • Comparing and aggregating partially resolved trees
    • Bansal,M.S. et al. (2008) Comparing and aggregating partially resolved trees. Lect. Notes Comput. Sci., 4957, 72-83.
    • (2008) Lect. Notes Comput. Sci. , vol.4957 , pp. 72-83
    • Bansal, M.S.1
  • 3
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • Baum,B.R. (1992) Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees. Taxon, 41, 3-10.
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.R.1
  • 4
    • 33751214516 scopus 로고    scopus 로고
    • A higher-level MRP supertree of placental mammals
    • Beck,R.M.D. et al. (2006) A higher-level MRP supertree of placental mammals. BMC Evol. Biol., 6, 93.
    • (2006) BMC Evol. Biol. , vol.6 , pp. 93
    • Beck, R.M.D.1
  • 5
    • 1642528337 scopus 로고    scopus 로고
    • Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees
    • Bininda-Emonds,O.R.P. (2003) Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Syst. Biol., 52, 839-848.
    • (2003) Syst. Biol. , vol.52 , pp. 839-848
    • Bininda-Emonds, O.R.P.1
  • 6
    • 34047108602 scopus 로고    scopus 로고
    • The delayed rise of present-day mammals
    • Bininda-Emonds,O.R.P. et al. (2007) The delayed rise of present-day mammals. Nature, 446, 507-512.
    • (2007) Nature , vol.446 , pp. 507-512
    • Bininda-Emonds, O.R.P.1
  • 7
    • 65349177696 scopus 로고    scopus 로고
    • Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades
    • Blanga-Kanfi,S. et al. (2009) Rodent phylogeny revised: analysis of six nuclear genes from all major rodent clades. BMC Evol. Biol., 9,71.
    • (2009) BMC Evol. Biol. , vol.9 , pp. 71
    • Blanga-Kanfi, S.1
  • 8
    • 13844266486 scopus 로고    scopus 로고
    • On the computational complexity of the rooted subtree prune and regraft distance
    • Bordewich,M. and Semple,C. (2004) On the computational complexity of the rooted subtree prune and regraft distance. Ann. Combinat., 8, 409-423.
    • (2004) Ann. Combinat. , vol.8 , pp. 409-423
    • Bordewich, M.1    Semple, C.2
  • 11
    • 1642519173 scopus 로고    scopus 로고
    • Aclassification of consensus methods for phylogenies
    • Janowitz,M. et al. (eds), DIMACS, AMS, Providence, RI
    • Bryant,D. (2003)Aclassification of consensus methods for phylogenies. In Janowitz,M. et al. (eds), Bioconsensus. DIMACS, AMS, Providence, RI, pp. 163-184.
    • (2003) Bioconsensus , pp. 163-184
    • Bryant, D.1
  • 12
    • 33747375683 scopus 로고    scopus 로고
    • Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome scale data
    • Burleigh,J.G. et al. (2006) Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome scale data. Syst. Biol., 55, 426-440.
    • (2006) Syst. Biol. , vol.55 , pp. 426-440
    • Burleigh, J.G.1
  • 13
    • 66049159777 scopus 로고    scopus 로고
    • Mosaic retroposon insertion patterns in placental mammals
    • Churakov,G. et al. (2009) Mosaic retroposon insertion patterns in placental mammals. Genome Res., 19, 868-875.
    • (2009) Genome Res. , vol.19 , pp. 868-875
    • Churakov, G.1
  • 14
    • 34548566074 scopus 로고    scopus 로고
    • Majority-rule supertrees
    • Cotton,J.A. and Wilkinson,M. (2007) Majority-rule supertrees. Syst. Biol., 56, 445-452.
    • (2007) Syst. Biol. , vol.56 , pp. 445-452
    • Cotton, J.A.1    Wilkinson, M.2
  • 15
    • 33745007116 scopus 로고    scopus 로고
    • Discriminating supported and unsupported relationships in supertrees using triplets
    • Cotton,J.A. et al. (2006) Discriminating supported and unsupported relationships in supertrees using triplets. Syst. Biol., 55, 345-350.
    • (2006) Syst. Biol. , vol.55 , pp. 345-350
    • Cotton, J.A.1
  • 16
    • 13844250623 scopus 로고    scopus 로고
    • CLANN: investigating phylogenetic information through supertree analyses
    • Creevey,C.J. and McInerney,J.O. (2005) CLANN: investigating phylogenetic information through supertree analyses. Bioinformatics, 21, 390-392.
    • (2005) Bioinformatics , vol.21 , pp. 390-392
    • Creevey, C.J.1    McInerney, J.O.2
  • 17
    • 34447341925 scopus 로고    scopus 로고
    • SDM: a fast distance-based approach for (super)tree building in phylogenomics
    • Criscuolo,A. et al. (2006) SDM: a fast distance-based approach for (super)tree building in phylogenomics. Syst. Biol., 55, 740-755.
    • (2006) Syst. Biol. , vol.55 , pp. 740-755
    • Criscuolo, A.1
  • 18
    • 0030311519 scopus 로고    scopus 로고
    • The triples distance for rooted bifurcating phylogenetic trees
    • Critchlow,D.E. et al. (1996) The triples distance for rooted bifurcating phylogenetic trees. Syst. Biol., 45, 323-334.
    • (1996) Syst. Biol. , vol.45 , pp. 323-334
    • Critchlow, D.E.1
  • 20
    • 0040400455 scopus 로고
    • Comparing the shapes of trees
    • Street,A.P. and Wallis,W.D. (eds) Springer, New York
    • Dobson,A.J. (1975) Comparing the shapes of trees. In Street,A.P. and Wallis,W.D. (eds) Combinatorial Mathematics III, LNCS, vol. 452. Springer, New York, pp. 95-100.
    • (1975) Combinatorial Mathematics III, LNCS , vol.452 , pp. 95-100
    • Dobson, A.J.1
  • 21
    • 0037329108 scopus 로고    scopus 로고
    • Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability
    • Douady,C.J. et al. (2003) Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability. Mol. Biol. Evol., 20, 248-254.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 248-254
    • Douady, C.J.1
  • 22
    • 0000989175 scopus 로고
    • Gene trees and species trees: molecular systematics as one-character taxonomy
    • Doyle,J.J. (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Syst. Bot., 17, 144-163.
    • (1992) Syst. Bot. , vol.17 , pp. 144-163
    • Doyle, J.J.1
  • 23
    • 2442598026 scopus 로고    scopus 로고
    • Performance of flip supertree construction with a heuristic algorithm
    • Eulenstein,O. et al. (2004) Performance of flip supertree construction with a heuristic algorithm. Syst. Biol., 53, 299-308.
    • (2004) Syst. Biol. , vol.53 , pp. 299-308
    • Eulenstein, O.1
  • 24
    • 84963088905 scopus 로고
    • A numerical approach to phylogenetic systematics
    • Farris,J.S. et al. (1970) A numerical approach to phylogenetic systematics. Syst. Zool., 19, 172-191.
    • (1970) Syst. Zool. , vol.19 , pp. 172-191
    • Farris, J.S.1
  • 26
    • 43449099081 scopus 로고    scopus 로고
    • An introduction to ROC analysis
    • Fawcett,T. (2005) An introduction to ROC analysis. Pattern Recogn. Lett., 27, 86-874.
    • (2005) Pattern Recogn. Lett. , vol.27 , pp. 86-874
    • Fawcett, T.1
  • 27
    • 45749124657 scopus 로고    scopus 로고
    • TNT, a free program for phylogenetic analysis
    • Goloboff,P.A. et al. (2008) TNT, a free program for phylogenetic analysis. Cladistics, 24, 774-786.
    • (2008) Cladistics , vol.24 , pp. 774-786
    • Goloboff, P.A.1
  • 28
    • 0000803938 scopus 로고
    • Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves
    • Gordon,A.D. (1986) Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. J. Classif., 3, 335-348.
    • (1986) J. Classif. , vol.3 , pp. 335-348
    • Gordon, A.D.1
  • 29
    • 34547119574 scopus 로고    scopus 로고
    • Closure operations in phylogenetics
    • Grunewald,S. et al. (2007) Closure operations in phylogenetics. Math. Biosci., 208, 521-537.
    • (2007) Math. Biosci. , vol.208 , pp. 521-537
    • Grunewald, S.1
  • 30
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood
    • Guindon,S. and Gascuel,O. (2003) A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol., 52, 696-704.
    • (2003) Syst. Biol. , vol.52 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 31
    • 0001996348 scopus 로고
    • The probabilities of rooted tree-shapes generated by random bifurcation
    • Harding,E. (1971) The probabilities of rooted tree-shapes generated by random bifurcation. Adv. Appl. Probab., 3, 44-77.
    • (1971) Adv. Appl. Probab. , vol.3 , pp. 44-77
    • Harding, E.1
  • 32
    • 41049096780 scopus 로고    scopus 로고
    • SPR distance computation of unrooted trees
    • Hickey,G. et al. (2008) SPR distance computation of unrooted trees. Evol. Bioinform. Online, 4, 17-27.
    • (2008) Evol. Bioinform. Online , vol.4 , pp. 17-27
    • Hickey, G.1
  • 33
    • 38449121762 scopus 로고    scopus 로고
    • Molecular and genomic data identify the closest living relative of primates
    • Janecka,J.E. et al. (2007) Molecular and genomic data identify the closest living relative of primates. Science, 318, 792-794.
    • (2007) Science , vol.318 , pp. 792-794
    • Janecka, J.E.1
  • 34
    • 33645850710 scopus 로고    scopus 로고
    • Phylogenomics: the beginning of incongruence?
    • Jeffroy,O. et al. (2006) Phylogenomics: the beginning of incongruence? Trends Genet., 22, 225-231.
    • (2006) Trends Genet , vol.22 , pp. 225-231
    • Jeffroy, O.1
  • 35
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • Kimura,M. (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 2, 87-90.
    • (1980) J. Mol. Evol. , vol.2 , pp. 87-90
    • Kimura, M.1
  • 36
    • 60849128510 scopus 로고    scopus 로고
    • Triplet supertree heuristics for the tree of life
    • Lin,H.T. et al. (2009) Triplet supertree heuristics for the tree of life. BMC Bioinformatics, 10(Suppl. 1), S8.
    • (2009) BMC Bioinformatics , vol.10 , Issue.SUPPL. 1
    • Lin, H.T.1
  • 37
    • 0024940670 scopus 로고
    • Reconstructing character evolution on polytomous cladograms
    • Maddison,W.P. (1989) Reconstructing character evolution on polytomous cladograms. Cladistics, 5, 365-377.
    • (1989) Cladistics , vol.5 , pp. 365-377
    • Maddison, W.P.1
  • 38
    • 33751227478 scopus 로고    scopus 로고
    • Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping
    • Moore,B.R. et al. (2006) Increasing data transparency and estimating phylogenetic uncertainty in supertrees: approaches using nonparametric bootstrapping. Syst. Biol., 55, 662-676.
    • (2006) Syst. Biol. , vol.55 , pp. 662-676
    • Moore, B.R.1
  • 39
    • 33646203435 scopus 로고    scopus 로고
    • Using semi-definite programming to enhance supertree resolvability
    • Istrail,S. et al. (eds) of LNCS, Springer, Berlin, ALLEMAGNE
    • Moran,S. et al. (2005) Using semi-definite programming to enhance supertree resolvability. In Istrail,S. et al. (eds) Algorithms in Bioinformatics, Proceedings of WABI 2005, Vol. 3692 of LNCS, Springer, Berlin, ALLEMAGNE, pp. 89-103.
    • (2005) Algorithms in Bioinformatics, Proceedings of WABI 2005 , vol.3692 , pp. 89-103
    • Moran, S.1
  • 40
    • 84928160511 scopus 로고    scopus 로고
    • PhD Thesis, University of Aarhus, Aarhus, Denmark
    • Mosses,C. (2005) Triplet supertrees. PhD Thesis, University of Aarhus, Aarhus, Denmark.
    • (2005) Triplet supertrees
    • Mosses, C.1
  • 41
    • 0000887481 scopus 로고
    • Three-item consensus: empirical test of fractional weighting
    • Scotland,R.W. et al. (eds) Clarendon, Oxford
    • Nelson,G. and Ladiges,P.Y. (1994) Three-item consensus: empirical test of fractional weighting. In Scotland,R.W. et al. (eds) Models in Phylogeny Reconstruction. Clarendon, Oxford, pp. 193-209.
    • (1994) Models in Phylogeny Reconstruction , pp. 193-209
    • Nelson, G.1    Ladiges, P.Y.2
  • 42
    • 84956992917 scopus 로고    scopus 로고
    • Guigó,R. and Gusfield,D. (eds) of LNCS, Springer, London, UK
    • Page,R.D.M. (2002) Modified MinCut supertrees. In Guigó,R. and Gusfield,D. (eds) Vol. 2452 of LNCS, Springer, London, UK, pp. 537-551.
    • (2002) Modified MinCut supertrees , vol.2452 , pp. 537-551
    • Page, R.D.M.1
  • 43
    • 0042014724 scopus 로고    scopus 로고
    • The asymmetric median tree-a new model for building consensus trees
    • Phillips,C. and Warnow,T.J. (1996) The asymmetric median tree-a new model for building consensus trees. Discr. Appl. Math., 71, 311-355.
    • (1996) Discr. Appl. Math. , vol.71 , pp. 311-355
    • Phillips, C.1    Warnow, T.J.2
  • 45
    • 49749129961 scopus 로고    scopus 로고
    • Confirming the phylogeny of mammals by use of large comparative sequence data sets
    • Prasad,A.B. et al. (2008) Confirming the phylogeny of mammals by use of large comparative sequence data sets. Mol. Biol. Evol., 25, 1795-1808.
    • (2008) Mol. Biol. Evol. , vol.25 , pp. 1795-1808
    • Prasad, A.B.1
  • 46
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • Ragan,M.A. (1992) Phylogenetic inference based on matrix representation of trees. Mol. Phyl. Evol., 1, 53-58.
    • (1992) Mol. Phyl. Evol. , vol.1 , pp. 53-58
    • Ragan, M.A.1
  • 47
    • 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. (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
  • 48
    • 39749111875 scopus 로고    scopus 로고
    • OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics
    • Ranwez,V. et al. (2007) OrthoMaM: a database of orthologous genomic markers for placental mammal phylogenetics. BMC Evol. Biol., 7,241.
    • (2007) BMC Evol. Biol. , vol.7 , pp. 241
    • Ranwez, V.1
  • 49
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • Robinson,D.F. and Foulds,L.R. (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
  • 50
    • 0023375195 scopus 로고
    • The neighbor-joining method: a new method for reconstructing phylogenetic trees
    • Saitou,N. and Nei,M. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 51
    • 0037314098 scopus 로고    scopus 로고
    • r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock
    • Sanderson,M.J. (2003) r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 19, 301-302.
    • (2003) Bioinformatics , vol.19 , pp. 301-302
    • Sanderson, M.J.1
  • 52
  • 53
    • 12044252586 scopus 로고
    • Distribution of tree comparison metrices - some new results
    • Steel,M.A. and Penny,D. (1993) Distribution of tree comparison metrices - some new results. Syst. Biol., 42, 126-141.
    • (1993) Syst. Biol. , vol.42 , pp. 126-141
    • Steel, M.A.1    Penny, D.2
  • 54
    • 41849131023 scopus 로고    scopus 로고
    • Maximum likelihood supertree
    • Steel,M.A. and Rodrigo, A. (2008) Maximum likelihood supertree. Syst. Biol., 57, 243-250.
    • (2008) Syst. Biol. , vol.57 , pp. 243-250
    • Steel, M.A.1    Rodrigo, A.2
  • 55
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Hillis, D.M. et al. (eds) Sinauer Associates, Massachussets
    • Swofford,D.L. et al. (1996) Phylogenetic inference. In Hillis, D.M. et al. (eds) Molecular Systematics. Sinauer Associates, Massachussets, pp. 407-514.
    • (1996) Molecular Systematics , pp. 407-514
    • Swofford, D.L.1
  • 57
    • 84989449521 scopus 로고
    • Three-taxon statements: when is a parsimony analysis also a clique analysis?
    • Wilkinson,M. (1994)Three-taxon statements: when is a parsimony analysis also a clique analysis? Cladistics, 10, 221-223.
    • (1994) Cladistics , vol.10 , pp. 221-223
    • Wilkinson, M.1
  • 58
    • 0001885156 scopus 로고    scopus 로고
    • Towards a phylogenetic supertree for platyhelminthes?
    • Littlewood,D.T. and Bray,R.A. (eds) Taylor and Francis, Chapman Hall, London
    • Wilkinson,M. et al. (2001) Towards a phylogenetic supertree for platyhelminthes? In Littlewood,D.T. and Bray,R.A. (eds) Interrelationships of the Platyhelminthes. Taylor and Francis, Chapman Hall, London, pp. 292-301.
    • (2001) Interrelationships of the Platyhelminthes , pp. 292-301
    • Wilkinson, M.1
  • 59
    • 12444265837 scopus 로고    scopus 로고
    • The information content of trees and their matrix representations
    • Wilkinson,M. et al. (2004) The information content of trees and their matrix representations. Syst. Biol., 53, 989-1001.
    • (2004) Syst. Biol. , vol.53 , pp. 989-1001
    • Wilkinson, M.1
  • 60
    • 22844442070 scopus 로고    scopus 로고
    • The shape of supertrees to come: tree shape related properties of fourteen supertree methods
    • Wilkinson,M. et al. (2005a) The shape of supertrees to come: tree shape related properties of fourteen supertree methods. Syst. Biol., 54, 419-431.
    • (2005) Syst. Biol. , vol.54 , pp. 419-431
    • Wilkinson, M.1
  • 61
    • 31344435061 scopus 로고    scopus 로고
    • Measuring support and finding unsupported relationships in supertrees
    • Wilkinson,M. et al. (2005b) Measuring support and finding unsupported relationships in supertrees. Syst. Biol., 54, 823-831.
    • (2005) Syst. Biol. , vol.54 , pp. 823-831
    • Wilkinson, M.1
  • 62
    • 34447284787 scopus 로고    scopus 로고
    • Properties of supertree methods in the consensus setting
    • Wilkinson,M. et al. (2007) Properties of supertree methods in the consensus setting. Syst. Biol., 56, 330-337.
    • (2007) Syst. Biol. , vol.56 , pp. 330-337
    • Wilkinson, M.1
  • 63
    • 12444299189 scopus 로고    scopus 로고
    • Supertrees, components and three-item data
    • Bininda-Emonds,O.R.P. (ed) Kluwer Academic Publishers, Dordrecht
    • Williams,D.M. (2004) Supertrees, components and three-item data. In Bininda-Emonds,O.R.P. (ed) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Kluwer Academic Publishers, Dordrecht, pp. 389-408.
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life , pp. 389-408
    • Williams, D.M.1
  • 64
    • 0037617885 scopus 로고    scopus 로고
    • Component coding, three-item coding, and consensus methods
    • Williams,D.M. and Humphries,C.J. (2003) Component coding, three-item coding, and consensus methods. Syst. Biol., 52, 255-259.
    • (2003) Syst. Biol. , vol.52 , pp. 255-259
    • Williams, D.M.1    Humphries, C.J.2
  • 65
    • 0001778604 scopus 로고
    • A mathematical theory of evolution, based on the conclusions of Dr J C. Willis. Philos
    • Yule,G.U. (1925) A mathematical theory of evolution, based on the conclusions of Dr J.C. Willis. Philos. Trans. Roy. Soc. B, 213, 21-87.
    • (1925) Trans. Roy. Soc. B , vol.213 , pp. 21-87
    • Yule, G.U.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.