메뉴 건너뛰기




Volumn 10, Issue 6, 2013, Pages 1432-1441

Efficient algorithms for knowledge-enhanced supertree and supermatrix phylogenetic problems

Author keywords

Phylogenetics; Supermatrix; Supertree

Indexed keywords

ALGORITHM; ARTICLE; ARTIFICIAL INTELLIGENCE; BIOLOGY; CLUSTER ANALYSIS; COMPUTER PROGRAM; GENE DUPLICATION; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

EID: 84894601642     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.162     Document Type: Article
Times cited : (11)

References (42)
  • 1
    • 57149107977 scopus 로고    scopus 로고
    • Introduction. Statistical and computational challenges in molecular phylogenetics and evolution
    • N. Goldman and Z. Yang, "Introduction. Statistical and Computational Challenges in Molecular Phylogenetics and Evolution," Philosophical Trans. of the Royal Soc. B: Biological Sciences, vol. 363, no. 1512, pp. 3889-3892, 2008.
    • (2008) Philosophical Trans. of the Royal Soc. B: Biological Sciences , vol.363 , Issue.1512 , pp. 3889-3892
    • Goldman, N.1    Yang, Z.2
  • 4
    • 33845627286 scopus 로고    scopus 로고
    • The supermatrix approach to systematics
    • DOI 10.1016/j.tree.2006.10.002, PII S0169534706003326
    • A. de Queiroz and J. Gatesy, "The Supermatrix Approach to Systematics," Trends in Ecology &Evolution, vol. 22, no. 1, pp. 34- 41, 2007. (Pubitemid 44959174)
    • (2007) Trends in Ecology and Evolution , vol.22 , Issue.1 , pp. 34-41
    • De Queiroz, A.1    Gatesy, J.2
  • 5
    • 0001614769 scopus 로고
    • The median procedure for n-trees
    • J. Barthélemy and F. McMorris, "The Median Procedure for N-Trees," J. Classification, vol. 3, no. 2, pp. 329-334, 1986.
    • (1986) J. Classification , vol.3 , Issue.2 , pp. 329-334
    • Barthélemy, J.1    McMorris, F.2
  • 6
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • DOI 10.1137/S0097539798343362, PII S0097539798343362
    • B. Ma, M. Li, and L. Zhang, "From Gene Trees to Species Trees," SIAM J. Computing, vol. 30, no. 3, pp. 729-752, 2001. (Pubitemid 32644732)
    • (2001) SIAM Journal on Computing , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 7
    • 80052886059 scopus 로고    scopus 로고
    • From gene trees to species trees II: Species tree inference in the deep coalescence model
    • L. Zhang, "From Gene Trees to Species Trees II: Species Tree Inference in the Deep Coalescence Model," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 1685- 1691, 2011.
    • (2011) IEEE/ACM Trans. Computational Biology and Bioinformatics , vol.8 , Issue.6 , pp. 1685-1691
    • Zhang, L.1
  • 8
    • 79952845540 scopus 로고    scopus 로고
    • A note on the fixed parameter tractability of the gene-duplication problem
    • May/June
    • M. Bansal and R. Shamir, "A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 3, pp. 848-850, May/June 2011.
    • (2011) IEEE/ACM Trans. Computational Biology and Bioinformatics , vol.8 , Issue.3 , pp. 848-850
    • Bansal, M.1    Shamir, R.2
  • 10
    • 79952845540 scopus 로고    scopus 로고
    • A note on the fixed parameter tractability of the gene-duplication problem
    • May/June
    • M. Bansal and R. Shamir, "A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 3, pp. 848-850, May/June 2011.
    • (2011) IEEE/ACM Trans. Computational Biology and Bioinformatics , vol.8 , Issue.3 , pp. 848-850
    • Bansal, M.1    Shamir, R.2
  • 11
    • 75149135738 scopus 로고    scopus 로고
    • Efficient genome- scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
    • article S42
    • M. Bansal, J. Burleigh, and O. Eulenstein, "Efficient Genome- Scale Phylogenetic Analysis under the Duplication-Loss and Deep Coalescence Cost Models," BMC Bioinformatics, vol. 11, no. Suppl 1, article S42, 2010.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 SUPPL.
    • Bansal, M.1    Burleigh, J.2    Eulenstein, O.3
  • 13
    • 67549131988 scopus 로고    scopus 로고
    • The gene-duplication problem: Near-linear time algorithms for nni-based local searches
    • Apr.-June
    • M. Bansal, O. Eulenstein, and A. Wehe, "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 221-231, Apr.-June 2009.
    • (2009) IEEE/ACM Trans. Computational Biology and Bioinformatics , vol.6 , Issue.2 , pp. 221-231
    • Bansal, M.1    Eulenstein, O.2    Wehe, A.3
  • 16
    • 33644606488 scopus 로고    scopus 로고
    • Inferring phylogeny despite incomplete lineage sorting
    • W. Maddison and L. Knowles, "Inferring Phylogeny Despite Incomplete Lineage Sorting," Systematic Biology, vol. 55, no. 1, pp. 21-30, 2006.
    • (2006) Systematic Biology , vol.55 , Issue.1 , pp. 21-30
    • Maddison, W.1    Knowles, L.2
  • 17
    • 46249126320 scopus 로고    scopus 로고
    • DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
    • DOI 10.1093/bioinformatics/btn230
    • A. Wehe, M. Bansal, J. Burleigh, and O. Eulenstein, "DupTree: A Program for Large-Scale Phylogenetic Analyses Using Gene Tree Parsimony," Bioinformatics, vol. 24, no. 13, pp. 1540-1541, 2008. (Pubitemid 351911710)
    • (2008) Bioinformatics , vol.24 , Issue.13 , pp. 1540-1541
    • Wehe, A.1    Bansal, M.S.2    Burleigh, J.G.3    Eulenstein, O.4
  • 18
    • 23144442051 scopus 로고    scopus 로고
    • TNT: Tree analysis using new technology
    • G. Giribet, "TNT: Tree Analysis Using New Technology," Systematic Biology, vol. 54, no. 1, pp. 176-178, 2005.
    • (2005) Systematic Biology , vol.54 , Issue.1 , pp. 176-178
    • Giribet, G.1
  • 20
    • 33750403801 scopus 로고    scopus 로고
    • RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
    • DOI 10.1093/bioinformatics/btl446
    • A. Stamatakis, "RAxML-VI-HPC: Maximum Likelihood-Based Phylogenetic Analyses with Thousands of Taxa and Mixed Models," Bioinformatics, vol. 22, no. 21, pp. 2688-2690, 2006. (Pubitemid 44642609)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2688-2690
    • Stamatakis, A.1
  • 22
    • 50249100595 scopus 로고    scopus 로고
    • A rapid bootstrap algorithm for the RAxML web servers
    • A. Stamatakis, P. Hoover, and J. Rougemont, "A Rapid Bootstrap Algorithm for the RAxML Web Servers," Systematic Biology, vol. 57, no. 5, pp. 758-771, 2008.
    • (2008) Systematic Biology , vol.57 , Issue.5 , pp. 758-771
    • Stamatakis, A.1    Hoover, P.2    Rougemont, J.3
  • 24
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • M. Goodman, J. Czelusniak, G. Moore, A. Romero-Herrera, and G. Matsuda, "Fitting the Gene Lineage into Its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences," Systematic Biology, vol. 28, no. 2, pp. 132-163, 1979.
    • (1979) Systematic Biology , vol.28 , Issue.2 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.3    Romero-Herrera, A.4    Matsuda, G.5
  • 25
    • 0030253222 scopus 로고    scopus 로고
    • Reconstruction of ancient molecular phylogeny
    • DOI 10.1006/mpev.1996.0071
    • R. Guigo, I. Muchnik, and T. Smith, "Reconstruction of Ancient Molecular Phylogeny," Molecular Phylogenetics and Evolution, vol. 6, no. 2, pp. 189-213, 1996. (Pubitemid 126320615)
    • (1996) Molecular Phylogenetics and Evolution , vol.6 , Issue.2 , pp. 189-213
    • Guigo, R.1    Muchnik, I.2    Smith, T.F.3
  • 26
    • 0031110886 scopus 로고    scopus 로고
    • From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem
    • DOI 10.1006/mpev.1996.0390, PII S1055790396903905
    • R. Page and M. Charleston, "From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem," Molecular Phylogenetics and Evolution, vol. 7, no. 2, pp. 231-240, 1997. (Pubitemid 127345887)
    • (1997) Molecular Phylogenetics and Evolution , vol.7 , Issue.2 , pp. 231-240
    • Page, R.D.M.1    Charleston, M.A.2
  • 27
    • 0033278654 scopus 로고    scopus 로고
    • How should species phylogenies be inferred from sequence data?
    • J. Slowinski and R. Page, "How Should Species Phylogenies be Inferred from Sequence Data?" Systematic Biology, vol. 48, no. 4, pp. 814-825, 1999. (Pubitemid 129490565)
    • (1999) Systematic Biology , vol.48 , Issue.4 , pp. 814-825
    • Slowinski, J.B.1    Page, R.D.M.2
  • 29
    • 0002844544 scopus 로고
    • Combining trees as a way of combining data sets for phylogenetic inference, and the desirability of combining gene trees
    • B. Baum, "Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees," Taxon, vol. 41, pp. 3-10, 1992.
    • (1992) Taxon , vol.41 , pp. 3-10
    • Baum, B.1
  • 30
    • 0026822436 scopus 로고
    • Phylogenetic inference based on matrix representation of trees
    • M. Ragan, "Phylogenetic Inference Based on Matrix Representation of Trees," Molecular Phylogenetics and Evolution, vol. 1, no. 1, pp. 53-58, 1992.
    • (1992) Molecular Phylogenetics and Evolution , vol.1 , Issue.1 , pp. 53-58
    • Ragan, M.1
  • 31
    • 0032030505 scopus 로고    scopus 로고
    • Phylogenetic supertrees: Assembling the trees of life
    • DOI 10.1016/S0169-5347(97)01242-1
    • M. Sanderson, A. Purvis, and C. Henze, "Phylogenetic Supertrees: Assembling the Trees of Life," Trends in Ecology &Evolution, vol. 13, no. 3, pp. 105-109, 1998. (Pubitemid 28136253)
    • (1998) Trends in Ecology and Evolution , vol.13 , Issue.3 , pp. 105-109
    • Sanderson, M.J.1    Purvis, A.2    Henze, C.3
  • 33
    • 0019424782 scopus 로고
    • Comparison of phylogenetic trees
    • DOI 10.1016/0025-5564(81)90043-2
    • D. Robinson and L. Foulds, "Comparison of Phylogenetic Trees," Math. Biosciences, vol. 53, no. 1/2, pp. 131-147, 1981. (Pubitemid 11129084)
    • (1981) Mathematical Biosciences , vol.53 , Issue.1-2 , pp. 131-147
    • Robinson, D.F.1    Foulds, L.R.2
  • 34
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescences
    • article e1000501
    • C. Than and L. Nakhleh, "Species Tree Inference by Minimizing Deep Coalescences," PLoS Computational Biology, vol. 5, no. 9, article e1000501, 2009.
    • (2009) PLoS Computational Biology , vol.5 , Issue.9
    • Than, C.1    Nakhleh, L.2
  • 35
    • 80955136714 scopus 로고    scopus 로고
    • Algorithms for MDC-based multi-locus phylogeny inference: Beyond rooted binary gene trees on single alleles
    • Y. Yu, T. Warnow, and L. Nakhleh, "Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles," J. Computational Biology, vol. 18, pp. 1543- 1559, 2011.
    • (2011) J. Computational Biology , vol.18 , pp. 1543-1559
    • Yu, Y.1    Warnow, T.2    Nakhleh, L.3
  • 37
    • 0016424695 scopus 로고
    • Minimal mutation trees of sequences
    • D. Sankoff, "Minimal Mutation Trees of Sequences," SIAM J. Applied Math., vol. 28, pp. 35-42, 1975.
    • (1975) SIAM J. Applied Math. , vol.28 , pp. 35-42
    • Sankoff, D.1
  • 38
    • 0000459582 scopus 로고
    • Locating the vertices of a steiner tree in an arbitrary metric space
    • D. Sankoff and P. Rousseau, "Locating the Vertices of a Steiner Tree in an Arbitrary Metric Space," Math. Programming, vol. 9, no. 1, pp. 240-246, 1975.
    • (1975) Math. Programming , vol.9 , Issue.1 , pp. 240-246
    • Sankoff, D.1    Rousseau, P.2
  • 39
    • 4544357678 scopus 로고    scopus 로고
    • A species-level phylogenetic supertree of marsupials
    • DOI 10.1017/S0952836904005539
    • M. Cardillo, R. Bininda-Emonds, E. Boakes, and A. Purvis, "A Species-Level Phylogenetic Supertree of Marsupials," J. Zoology, vol. 264, no. 1, pp. 11-31, 2004. (Pubitemid 39246912)
    • (2004) Journal of Zoology , vol.264 , Issue.1 , pp. 11-31
    • Cardillo, M.1    Bininda-Emonds, O.R.P.2    Boakes, E.3    Purvis, A.4
  • 40
    • 84861137137 scopus 로고    scopus 로고
    • Exploring diversification and genome size evolution in extant gymnosperms through phylogenetic synthesis
    • article 292854
    • J. Burleigh, W. Barbazuk, J. Davis, A. Morse, and P. Soltis, "Exploring Diversification and Genome Size Evolution in Extant Gymnosperms through Phylogenetic Synthesis," J. Botany, vol. 2012, article 292854, 2012.
    • (2012) J. Botany , vol.2012
    • Burleigh, J.1    Barbazuk, W.2    Davis, J.3    Morse, A.4    Soltis, P.5
  • 41
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • DOI 10.1006/clad.1999.0121
    • K. Nixon, "The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis," Cladistics, vol. 15, no. 4, pp. 407-414, 1999. (Pubitemid 30203167)
    • (1999) Cladistics , vol.15 , Issue.4 , pp. 407-414
    • Nixon, K.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.