메뉴 건너뛰기




Volumn , Issue , 2014, Pages 19-48

An introduction to supertree construction (and partitioned phylogenetic analyses) with a view toward the distinction between gene trees and species trees

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84957041360     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-662-43550-2_3     Document Type: Chapter
Times cited : (15)

References (100)
  • 1
    • 84959774562 scopus 로고
    • Consensus techniques and the comparison of taxonomic trees
    • Adams EM III (1972) Consensus techniques and the comparison of taxonomic trees. Syst Zool 21:390-397
    • (1972) Syst Zool , vol.21 , pp. 390-397
    • Adams, E.M.1
  • 2
    • 0000090670 scopus 로고
    • N-trees as nestings: Complexity, similarity, and consensus
    • Adams EM III (1986) N-trees as nestings: complexity, similarity, and consensus. J Classif 3:299-317
    • (1986) J Classif , vol.3 , pp. 299-317
    • Adams, E.M.1
  • 3
    • 77954574612 scopus 로고    scopus 로고
    • The 10k Trees website: A new online resource for primate phylogeny
    • Arnold CL, Matthews J, Nunn CL (2010) The 10k Trees website: a new online resource for primate phylogeny. Evol Anthropol 19:114-118
    • (2010) Evol Anthropol , vol.19 , pp. 114-118
    • Arnold, C.L.1    Matthews, J.2    Nunn, C.L.3
  • 5
    • 0031371067 scopus 로고    scopus 로고
    • Multiple sources of character information and the phylogeny of Hawaiian drosophilids
    • Baker RH, DeSalle R (1997) Multiple sources of character information and the phylogeny of Hawaiian drosophilids. Syst Biol 46:654-673
    • (1997) Syst Biol , vol.46 , pp. 654-673
    • Baker, R.H.1    Desalle, R.2
  • 7
    • 84957022957 scopus 로고
    • A book of whales. G.P. Putnam’s Sons, New York
    • Beddard FE (1900) A book of whales. G.P. Putnam’s Sons, New York
    • (1900)
    • Beddard, F.E.1
  • 8
    • 20444491634 scopus 로고    scopus 로고
    • A review of long-branch attraction
    • Bergsten J (2005) A review of long-branch attraction. Cladistics 21(2):163-193
    • (2005) Cladistics , vol.21 , Issue.2 , pp. 163-193
    • Bergsten, J.1
  • 9
    • 84873599883 scopus 로고    scopus 로고
    • Amalgamating source trees with different taxonomic levels
    • Berry V, Bininda-Emonds ORP, Semple C (2013) Amalgamating source trees with different taxonomic levels. Syst Biol 62(2):231-249
    • (2013) Syst Biol , vol.62 , Issue.2 , pp. 231-249
    • Berry, V.1    Bininda-Emonds, O.2    Semple, C.3
  • 10
    • 1642528337 scopus 로고    scopus 로고
    • Novel versus unsupported clades: Assessing the qualitative support for clades in MRP supertrees
    • Bininda-Emonds ORP (2003) Novel versus unsupported clades: assessing the qualitative support for clades in MRP supertrees. Syst Biol 52(6):839-848
    • (2003) Syst Biol , vol.52 , Issue.6 , pp. 839-848
    • Bininda-Emonds, O.1
  • 11
    • 2942600199 scopus 로고    scopus 로고
    • The evolution of supertrees
    • Bininda-Emonds ORP (2004a) The evolution of supertrees. Trends Ecol Evol 19(6):315-322
    • (2004) Trends Ecol Evol , vol.19 , Issue.6 , pp. 315-322
    • Bininda-Emonds, O.1
  • 13
    • 2442514172 scopus 로고    scopus 로고
    • Trees versus characters and the supertree/supermatrix “paradox”
    • Bininda-Emonds ORP (2004c) Trees versus characters and the supertree/supermatrix “paradox”. Syst Biol 53(2):356-359
    • (2004) Syst Biol , vol.53 , Issue.2 , pp. 356-359
    • Bininda-Emonds, O.1
  • 14
    • 84870311429 scopus 로고    scopus 로고
    • The future of supertrees: Bridging the gap with supermatrices
    • Bininda-Emonds ORP (2010) The future of supertrees: bridging the gap with supermatrices. Palaeodiversity 3(Suppl.):99-106
    • (2010) Palaeodiversity , vol.3 , pp. 99-106
    • Bininda-Emonds, O.1
  • 15
    • 80053107842 scopus 로고    scopus 로고
    • Inferring the Tree of Life: Chopping a phylogenomic problem down to size?
    • Bininda-Emonds ORP (2011) Inferring the Tree of Life: chopping a phylogenomic problem down to size? BMC Biol 9:59
    • (2011) BMC Biol , vol.9 , pp. 59
    • Bininda-Emonds, O.1
  • 16
    • 25144456389 scopus 로고    scopus 로고
    • Getting to the roots of matrix representation
    • Bininda-Emonds ORP, Beck RMD, Purvis A (2005) Getting to the roots of matrix representation. Syst Biol 54(4):668-672
    • (2005) Syst Biol , vol.54 , Issue.4 , pp. 668-672
    • Bininda-Emonds, O.1    Beck, R.2    Purvis, A.3
  • 17
    • 0032148631 scopus 로고    scopus 로고
    • Properties of matrix representation with parsimony analyses
    • Bininda-Emonds ORP, Bryant HN (1998) Properties of matrix representation with parsimony analyses. Syst Biol 47(3):497-508
    • (1998) Syst Biol , vol.47 , Issue.3 , pp. 497-508
    • Bininda-Emonds, O.1    Bryant, H.N.2
  • 20
    • 0035527411 scopus 로고    scopus 로고
    • Assessment of the accuracy of matrix representation with parsimony supertree construction
    • Bininda-Emonds ORP, Sanderson MJ (2001) Assessment of the accuracy of matrix representation with parsimony supertree construction. Syst Biol 50(4):565-579
    • (2001) Syst Biol , vol.50 , Issue.4 , pp. 565-579
    • Bininda-Emonds, O.1    Sanderson, M.J.2
  • 21
    • 0000367652 scopus 로고
    • The limits of amino acid sequence data in angiosperm phylogenetic reconstruction
    • Bremer K (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42:795-803
    • (1988) Evolution , vol.42 , pp. 795-803
    • Bremer, K.1
  • 22
    • 54549085607 scopus 로고    scopus 로고
    • Parsimony via consensus
    • Bruen TC, Bryant D (2008) Parsimony via consensus. Syst Biol 57(2):251-256
    • (2008) Syst Biol , vol.57 , Issue.2 , pp. 251-256
    • Bruen, T.C.1    Bryant, D.2
  • 23
    • 33747375683 scopus 로고    scopus 로고
    • Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets
    • Burleigh JG, Driskell AC, Sanderson MJ (2006) Supertree bootstrapping methods for assessing phylogenetic variation among genes in genome-scale data sets. Syst Biol 55(3):426-440
    • (2006) Syst Biol , vol.55 , Issue.3 , pp. 426-440
    • Burleigh, J.G.1    Driskell, A.C.2    Sanderson, M.J.3
  • 25
    • 0041599373 scopus 로고    scopus 로고
    • Flipping: A supertree construction method
    • Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS, DIMACS Series in discrete mathematics and theoretical computer scienceAmerican Mathematical Society, Providence, RI
    • Chen D, Diao L, Eulenstein O, Fernandez-Baca D, Sanderson MJ (2003) Flipping: a supertree construction method. In: Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS (eds) Bioconsensus, vol 61., DIMACS Series in discrete mathematics and theoretical computer scienceAmerican Mathematical Society, Providence, RI, pp 135-160
    • (2003) Bioconsensus, Vol 61. , pp. 135-160
    • Chen, D.1    Diao, L.2    Eulenstein, O.3    Fernandez-Baca, D.4    Sanderson, M.J.5
  • 26
    • 8844235682 scopus 로고    scopus 로고
    • Rainbow: A toolbox for phylogenetic supertree construction and analysis
    • Chen D, Eulenstein O, Fernandez-Baca D (2004) Rainbow: a toolbox for phylogenetic supertree construction and analysis. Bioinformatics 20(16):2872-2873
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2872-2873
    • Chen, D.1    Eulenstein, O.2    Fernandez-Baca, D.3
  • 27
    • 12044258419 scopus 로고
    • Weighting, partitioning, and combining characters in phylogenetic analysis
    • Chippindale PT, Wiens JJ (1994) Weighting, partitioning, and combining characters in phylogenetic analysis. Syst Biol 43:278-287
    • (1994) Syst Biol , vol.43 , pp. 278-287
    • Chippindale, P.T.1    Wiens, J.J.2
  • 28
    • 70350384647 scopus 로고    scopus 로고
    • Tangled trees from multiple markers: Reconciling conflict between phylogenies to build molecular supertrees
    • Bininda-Emonds ORP, Kluwer Academic, Dordrecht, the Netherlands
    • Cotton JA, Page RDM (2004) Tangled trees from multiple markers: reconciling conflict between phylogenies to build molecular supertrees. In: Bininda-Emonds ORP (ed) Phylogenetic supertrees: combining information to reveal the tree of life, computational biology, vol 4. Kluwer Academic, Dordrecht, the Netherlands, pp 107-125
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology , vol.4 , pp. 107-125
    • Cotton, J.A.1    Page, R.2
  • 29
    • 34548566074 scopus 로고    scopus 로고
    • Majority-rule supertrees
    • Cotton JA, Wilkinson M (2007) Majority-rule supertrees. Syst Biol 56(3):445-452
    • (2007) Syst Biol , vol.56 , Issue.3 , pp. 445-452
    • Cotton, J.A.1    Wilkinson, M.2
  • 30
    • 13844250623 scopus 로고    scopus 로고
    • Clann: Investigating phylogenetic information through supertree analyses
    • Creevey CJ, McInerney JO (2005) Clann: investigating phylogenetic information through supertree analyses. Bioinformatics 21(3):390-392
    • (2005) Bioinformatics , vol.21 , Issue.3 , pp. 390-392
    • Creevey, C.J.1    Mc Inerney, J.O.2
  • 32
    • 0001546577 scopus 로고
    • Separate versus combined analysis of phylogenetic evidence
    • de Queiroz A, Donoghue MJ, Kim J (1995) Separate versus combined analysis of phylogenetic evidence. Annu Rev Ecol Syst 26:657-681
    • (1995) Annu Rev Ecol Syst , vol.26 , pp. 657-681
    • De Queiroz, A.1    Donoghue, M.J.2    Kim, J.3
  • 33
    • 33646928341 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees
    • Degnan JH, Rosenberg NA (2006) Discordance of species trees with their most likely gene trees. PLoS Genet 2(5):762-768
    • (2006) Plos Genet , vol.2 , Issue.5 , pp. 762-768
    • Degnan, J.H.1    Rosenberg, N.A.2
  • 34
    • 58249100073 scopus 로고    scopus 로고
    • Is a new and general theory of molecular systematics emerging?
    • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63(1):1-19
    • (2009) Evolution , vol.63 , Issue.1 , pp. 1-19
    • Edwards, S.V.1
  • 35
    • 84963088905 scopus 로고
    • A numerical approach to phylogenetic systematics
    • Farris JS, Kluge AG, Eckhardt MJ (1970) A numerical approach to phylogenetic systematics. Syst Zool 19:172-191
    • (1970) Syst Zool , vol.19 , pp. 172-191
    • Farris, J.S.1    Kluge, A.G.2    Eckhardt, M.J.3
  • 36
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401-410
    • (1978) Syst Zool , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 37
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies: An approach using the bootstrap
    • Felsenstein J (1985a) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 38
    • 0022203256 scopus 로고
    • Phylogenies and the comparative method
    • Felsenstein J (1985b) Phylogenies and the comparative method. Am Nat 125:1-15
    • (1985) Am Nat , vol.125 , pp. 1-15
    • Felsenstein, J.1
  • 39
    • 0036698966 scopus 로고    scopus 로고
    • Resolution of a supertree/supermatrix paradox
    • Gatesy J, Matthee C, DeSalle R, Hayashi C (2002) Resolution of a supertree/supermatrix paradox. Syst Biol 51(4):652-664
    • (2002) Syst Biol , vol.51 , Issue.4 , pp. 652-664
    • Gatesy, J.1    Matthee, C.2    Desalle, R.3    Hayashi, C.4
  • 40
    • 0032805771 scopus 로고    scopus 로고
    • Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level artiodactyl taxa
    • Gatesy J, O’Grady P, Baker RH (1999) Corroboration among data sets in simultaneous analysis: hidden support for phylogenetic relationships among higher level artiodactyl taxa. Cladistics 15(3):271-313
    • (1999) Cladistics , vol.15 , Issue.3 , pp. 271-313
    • Gatesy, J.1    O’grady, P.2    Baker, R.H.3
  • 42
    • 84875547630 scopus 로고    scopus 로고
    • Concatenation versus coalescence versus “concatalescence”
    • USA
    • Gatesy J, Springer MS (2013) Concatenation versus coalescence versus “concatalescence”. Proc Natl Acad Sci USA 110(13):E1179-E1179
    • (2013) Proc Natl Acad Sci , vol.110 , Issue.13
    • Gatesy, J.1    Springer, M.S.2
  • 43
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool 28(2):132-163
    • (1979) Syst Zool , vol.28 , Issue.2 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 44
    • 0000803938 scopus 로고
    • Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves
    • Gordon AD (1986) Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labeled leaves. J Classif 3:31-39
    • (1986) J Classif , vol.3 , pp. 31-39
    • Gordon, A.D.1
  • 45
    • 0032025857 scopus 로고    scopus 로고
    • Is it better to add taxa or characters to a difficult phylogenetic problem?
    • Graybeal A (1998) Is it better to add taxa or characters to a difficult phylogenetic problem? Syst Biol 47(1):9-17
    • (1998) Syst Biol , vol.47 , Issue.1 , pp. 9-17
    • Graybeal, A.1
  • 48
    • 0023501273 scopus 로고
    • Molecular versus morphological approaches to systematics
    • Hillis DM (1987) Molecular versus morphological approaches to systematics. Annu Rev Ecol Syst 18:23-42
    • (1987) Annu Rev Ecol Syst , vol.18 , pp. 23-42
    • Hillis, D.M.1
  • 50
    • 84959806898 scopus 로고
    • A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes)
    • Kluge AG (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst Zool 38:7-25
    • (1989) Syst Zool , vol.38 , pp. 7-25
    • Kluge, A.G.1
  • 51
    • 84861380450 scopus 로고    scopus 로고
    • PartitionFinder: Combined selection of partitioning schemes and substitution models for phylogenetic analyses
    • Lanfear R, Calcott B, Ho SYW, Guindon S (2012) PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Mol Biol Evol 29(6):1695-1701
    • (2012) Mol Biol Evol , vol.29 , Issue.6 , pp. 1695-1701
    • Lanfear, R.1    Calcott, B.2    Ho, S.3    Guindon, S.4
  • 52
    • 0031513152 scopus 로고    scopus 로고
    • The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa
    • Lapointe F-J, Cucumel G (1997) The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst Biol 46(2):306-312
    • (1997) Syst Biol , vol.46 , Issue.2 , pp. 306-312
    • Lapointe, F.-J.1    Cucumel, G.2
  • 53
    • 0033072060 scopus 로고    scopus 로고
    • Total evidence, consensus, and bat phylogeny: A distance based approach
    • Lapointe F-J, Kirsch JAW, Hutcheon JM (1999) Total evidence, consensus, and bat phylogeny: a distance based approach. Mol Phylogenet Evol 11(1):55-66
    • (1999) Mol Phylogenet Evol , vol.11 , Issue.1 , pp. 55-66
    • Lapointe, F.-J.1    Kirsch, J.2    Hutcheon, J.M.3
  • 55
    • 70350393825 scopus 로고    scopus 로고
    • Strong morphological support for the molecular evolutionary tree of placental mammals
    • JEB1843 [pii]
    • Lee MS, Camens AB (2009) Strong morphological support for the molecular evolutionary tree of placental mammals. J Evol Biol 22 (11):2243-2257. doi:JEB1843 [pii] 10.1111/j.1420-9101.2009.01843.x
    • (2009) J Evol Biol , vol.22 , Issue.11 , pp. 2243-2257
    • Lee, M.S.1    Camens, A.B.2
  • 58
    • 77951961553 scopus 로고    scopus 로고
    • Phybase: An R package for species tree analysis
    • Liu L, Yu L (2010) Phybase: an R package for species tree analysis. Bioinformatics 26:962-963
    • (2010) Bioinformatics , vol.26 , pp. 962-963
    • Liu, L.1    Yu, L.2
  • 60
    • 70349425459 scopus 로고    scopus 로고
    • Estimating species phylogenies using coalescence times among sequences
    • Liu L, Yu LL, Pearl DK, Edwards SV (2009b) Estimating species phylogenies using coalescence times among sequences. Syst Biol 58(5):468-477
    • (2009) Syst Biol , vol.58 , Issue.5 , pp. 468-477
    • Liu, L.1    Yu, L.L.2    Pearl, D.K.3    Edwards, S.V.4
  • 61
    • 77957686501 scopus 로고    scopus 로고
    • A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
    • Liu LA, Yu LL, Edwards SV (2010) A maximum pseudo-likelihood approach for estimating species trees under the coalescent model. BMC Evol Biol 10
    • (2010) BMC Evol Biol , pp. 10
    • Liu, L.A.1    Yu, L.L.2    Edwards, S.V.3
  • 62
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison WP (1997) Gene trees in species trees. Syst Biol 46(3):523-536
    • (1997) Syst Biol , vol.46 , Issue.3 , pp. 523-536
    • Maddison, W.P.1
  • 65
    • 84863550128 scopus 로고    scopus 로고
    • Response to comment on “impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification”
    • Murphy WJ, Janecka JE, Stadler T, Eizirik E, Ryder OA, Gatesy J, Meredith RW, Springer MS (2012) Response to comment on “impacts of the cretaceous terrestrial revolution and KPg extinction on mammal diversification”. Science 337(6090):34
    • (2012) Science , vol.337 , Issue.6090 , pp. 34
    • Murphy, W.J.1    Janecka, J.E.2    Stadler, T.3    Eizirik, E.4    Ryder, O.A.5    Gatesy, J.6    Meredith, R.W.7    Springer, M.S.8
  • 66
    • 84856094866 scopus 로고    scopus 로고
    • MRL and SuperFine plus MRL: New supertree methods
    • Nguyen N, Mirarab S, Warnow T (2012) MRL and SuperFine plus MRL: new supertree methods. Algorithms Mol Biol 7(1):3
    • (2012) Algorithms Mol Biol , vol.7 , Issue.1 , pp. 3
    • Nguyen, N.1    Mirarab, S.2    Warnow, T.3
  • 67
    • 84857422378 scopus 로고    scopus 로고
    • Updating the evolutionary history of Carnivora (Mammalia): A new species-level supertree complete with divergence time estimates
    • Nyakatura K, Bininda-Emonds ORP (2012) Updating the evolutionary history of Carnivora (mammalia): a new species-level supertree complete with divergence time estimates. BMC Biol 10:12
    • (2012) BMC Biol , vol.10 , pp. 12
    • Nyakatura, K.1    Bininda-Emonds, O.2
  • 68
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • Page RDM (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst Biol 43(1):58-77
    • (1994) Syst Biol , vol.43 , Issue.1 , pp. 58-77
    • Page, R.1
  • 71
    • 0029653995 scopus 로고
    • A composite estimate of primate phylogeny
    • Ponstein J (1966) Matrices in graph and network theory. Van Gorcum, Assen, Netherlands Purvis A
    • Ponstein J (1966) Matrices in graph and network theory. Van Gorcum, Assen, Netherlands Purvis A (1995a) A composite estimate of primate phylogeny. Philos Trans R Soc Lond B 348:405-421
    • (1995) Philos Trans R Soc Lond B , vol.348 , pp. 405-421
  • 72
    • 0029495388 scopus 로고
    • A modification to Baum and Ragan’s method for combining phylogenetic trees
    • Purvis A (1995b) A modification to Baum and Ragan’s method for combining phylogenetic trees. Syst Biol 44:251-255
    • (1995) Syst Biol , vol.44 , pp. 251-255
    • Purvis, A.1
  • 73
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • Ragan MA (1992) Phylogenetic inference based on matrix representation of trees. Mol Phylogenet Evol 1:53-58
    • (1992) Mol Phylogenet Evol , vol.1 , pp. 53-58
    • Ragan, M.A.1
  • 74
    • 0041817551 scopus 로고    scopus 로고
    • Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    • Rannala B, Yang ZH (2003) Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164:1645-1656
    • (2003) Genetics , vol.164 , pp. 1645-1656
    • Rannala, B.1    Yang, Z.H.2
  • 76
    • 0033793019 scopus 로고    scopus 로고
    • Rare genomic changes as a tool for phylogenetics
    • Rokas A, Holland PW (2000) Rare genomic changes as a tool for phylogenetics. Trends Ecol Evol 15(11):454-459
    • (2000) Trends Ecol Evol , vol.15 , Issue.11 , pp. 454-459
    • Rokas, A.1    Holland, P.W.2
  • 77
    • 0030311386 scopus 로고    scopus 로고
    • Matrix representation of trees, redundancy, and weighting
    • Ronquist F (1996) Matrix representation of trees, redundancy, and weighting. Syst Biol 45:247-253
    • (1996) Syst Biol , vol.45 , pp. 247-253
    • Ronquist, F.1
  • 79
    • 84890335523 scopus 로고    scopus 로고
    • Discordance of species trees with their most likely gene trees: A unifying principle
    • Rosenberg NA (2013) Discordance of species trees with their most likely gene trees: a unifying principle. Mol Biol Evol 30(12):2709-2713. doi:10.1093/molbev/mst160
    • (2013) Mol Biol Evol , vol.30 , Issue.12 , pp. 2709-2713
    • Rosenberg, N.A.1
  • 81
    • 2942614199 scopus 로고    scopus 로고
    • An assessment of matrix representation with compatibility in supertree construction
    • Bininda-Emonds ORP, Kluwer Academic, Dordrecht, the Netherlands
    • Ross HA, Rodrigo AG (2004) An assessment of matrix representation with compatibility in supertree construction. In: Bininda-Emonds ORP (ed) Phylogenetic supertrees: combining information to reveal the tree of life, computational biology, vol 4. Kluwer Academic, Dordrecht, the Netherlands, pp 35-63
    • (2004) Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology , vol.4 , pp. 35-63
    • Ross, H.A.1    Rodrigo, A.G.2
  • 82
    • 0036005526 scopus 로고    scopus 로고
    • Building supertrees: An empirical assessment using the grass family (Poaceae)
    • Salamin N, Hodkinson TR, Savolainen V (2002) Building supertrees: an empirical assessment using the grass family (Poaceae). Syst Biol 51(1):136-150
    • (2002) Syst Biol , vol.51 , Issue.1 , pp. 136-150
    • Salamin, N.1    Hodkinson, T.R.2    Savolainen, V.3
  • 83
    • 0001354740 scopus 로고
    • TreeBASE: A prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life
    • Sanderson MJ, Donoghue MJ, Piel W, Eriksson T (1994) TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am J Bot 81(6):183
    • (1994) Am J Bot , vol.81 , Issue.6 , pp. 183
    • Sanderson, M.J.1    Donoghue, M.J.2    Piel, W.3    Eriksson, T.4
  • 84
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18(3):502-504
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 85
    • 55249091610 scopus 로고    scopus 로고
    • PhySIC_IST: Cleaning source trees to infer more informative supertrees
    • 1471-2105-9-413 [pii]
    • Scornavacca C, Berry V, Lefort V, Douzery EJ, Ranwez V (2008) PhySIC_IST: cleaning source trees to infer more informative supertrees. BMC Bioinformatics 9:413. doi:1471-2105-9-413 [pii] 10.1186/1471-2105-9-413
    • (2008) BMC Bioinformatics , vol.9 , pp. 413
    • Scornavacca, C.1    Berry, V.2    Lefort, V.3    Douzery, E.J.4    Ranwez, V.5
  • 86
    • 0001541744 scopus 로고    scopus 로고
    • A supertree method for rooted trees
    • Semple C, Steel M (2000) A supertree method for rooted trees. Discrete Appl Math 105(1—3):147—158
    • (2000) Discrete Appl Math , vol.105 , Issue.1-3 , pp. 147-158
    • Semple, C.1    Steel, M.2
  • 87
    • 79952762847 scopus 로고    scopus 로고
    • Understanding angiosperm diversification using small and large phylogenetic trees
    • Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ (2011) Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot 98(3):404-414
    • (2011) Am J Bot , vol.98 , Issue.3 , pp. 404-414
    • Smith, S.A.1    Beaulieu, J.M.2    Stamatakis, A.3    Donoghue, M.J.4
  • 88
    • 84866289853 scopus 로고    scopus 로고
    • Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
    • USA
    • Song S, Liu L, Edwards SV, Wu SY (2012) Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model. Proc Natl Acad Sci USA 109(37):14942-14947
    • (2012) Proc Natl Acad Sci , vol.109 , Issue.37 , pp. 14942-14947
    • Song, S.1    Liu, L.2    Edwards, S.V.3    Wu, S.Y.4
  • 89
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-analysis of large phylogenies
    • press
    • Stamatakis A (in press) RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics. doi:10.1093/bioinformatics/btu033
    • Bioinformatics
    • Stamatakis, A.1
  • 90
    • 0034350430 scopus 로고    scopus 로고
    • Simple but fundamental limitations on supertree and consensus tree methods
    • Steel M, Dress AWM, Böcker S (2000) Simple but fundamental limitations on supertree and consensus tree methods. Syst Biol 49(2):363-368
    • (2000) Syst Biol , vol.49 , Issue.2 , pp. 363-368
    • Steel, M.1    Dress, A.2    Böcker, S.3
  • 91
    • 41849131023 scopus 로고    scopus 로고
    • Maximum likelihood supertrees
    • Steel M, Rodrigo A (2008) Maximum likelihood supertrees. Syst Biol 57(2):243-250
    • (2008) Syst Biol , vol.57 , Issue.2 , pp. 243-250
    • Steel, M.1    Rodrigo, A.2
  • 92
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • Strimmer K, von Haeseler A (1996) Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies. Mol Biol Evol 13:964-969
    • (1996) Mol Biol Evol , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 93
    • 84857250162 scopus 로고    scopus 로고
    • SuperFine: Fast and accurate supertree estimation
    • Swenson MS, Suri R, Linder CR, Warnow T (2012) SuperFine: fast and accurate supertree estimation. Syst Biol 61(2):214-227
    • (2012) Syst Biol , vol.61 , Issue.2 , pp. 214-227
    • Swenson, M.S.1    Suri, R.2    Linder, C.R.3    Warnow, T.4
  • 95
    • 84883213635 scopus 로고    scopus 로고
    • Making the impossible possible: Rooting the tree of placental mammals
    • Teeling EC, Hedges SB (2013) Making the impossible possible: rooting the tree of placental mammals. Mol Biol Evol 30(9):1999-2000
    • (2013) Mol Biol Evol , vol.30 , Issue.9 , pp. 1999-2000
    • Teeling, E.C.1    Hedges, S.B.2
  • 96
    • 1642478458 scopus 로고    scopus 로고
    • A view of supertree methods
    • Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS, DIMACS series in discrete mathematics and theoretical computer scienceAmerican Mathematical Society, Providence, RI
    • Thorley JL, Wilkinson M (2003) A view of supertree methods. In: Janowitz MF, Lapointe F-J, McMorris FR, Mirkin B, Roberts FS (eds) Bioconsensus, vol 61., DIMACS series in discrete mathematics and theoretical computer scienceAmerican Mathematical Society, Providence, RI, pp 185-193
    • (2003) Bioconsensus , vol.61 , pp. 185-193
    • Thorley, J.L.1    Wilkinson, M.2
  • 97
    • 46249126320 scopus 로고    scopus 로고
    • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • Wehe A, Bansal MS, Burleigh JG, Eulenstein O (2008) DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540-1541
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 98
    • 31344435061 scopus 로고    scopus 로고
    • Measuring support and finding unsupported relationships in supertrees
    • Wilkinson M, Pisani D, Cotton JA, Corfe I (2005) Measuring support and finding unsupported relationships in supertrees. Syst Biol 54(5):823-831
    • (2005) Syst Biol , vol.54 , Issue.5 , pp. 823-831
    • Wilkinson, M.1    Pisani, D.2    Cotton, J.A.3    Corfe, I.4
  • 100
    • 84875513968 scopus 로고    scopus 로고
    • Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity
    • Wu SY, Song S, Liu L, Edwards SV (2013) Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity. Proc Natl Acad Sci USA 110(13):E1180-E1180
    • (2013) Proc Natl Acad Sci USA , vol.110 , Issue.13
    • Wu, S.Y.1    Song, S.2    Liu, L.3    Edwards, S.V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.