메뉴 건너뛰기




Volumn 29, Issue 3, 2005, Pages 196-203

Integer linear programming as a tool for constructing trees from quartet data

Author keywords

Integer linear programming; Mammals' mitochondrial evolution; Observed rate matrix; Phylogeny; Weighted quartet

Indexed keywords

ALGORITHMS; CELLS; GENETIC ENGINEERING; LINEAR PROGRAMMING; MATRIX ALGEBRA; MAXIMUM LIKELIHOOD ESTIMATION; OPTIMIZATION; PROBLEM SOLVING; TOPOLOGY; TREES (MATHEMATICS);

EID: 20444492866     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2005.04.001     Document Type: Article
Times cited : (8)

References (27)
  • 1
    • 34047267637 scopus 로고
    • A canonical decomposition theory for metrics on a finite set
    • H.-J. Bandelt, and A. Dress A canonical decomposition theory for metrics on a finite set Adv. Math. 92 1 1992 47 105
    • (1992) Adv. Math. , vol.92 , Issue.1 , pp. 47-105
    • Bandelt, H.-J.1    Dress, A.2
  • 2
    • 20444445039 scopus 로고
    • A relational approach to split decomposition
    • Materialien/Universität Bielefeld
    • Bandelt, H.-J., Dress, A., 1993. A relational approach to split decomposition. Materialien/Universität Bielefeld, Forschungsschwerpunkt Mathematisierung 68.
    • (1993) Forschungsschwerpunkt Mathematisierung , vol.68
    • Bandelt, H.-J.1    Dress, A.2
  • 3
    • 0031721805 scopus 로고    scopus 로고
    • Constructing phylogenies from quartets: Elucidation of eutherian superordinal relationships
    • A. Ben-Dor, B. Chor, D. Graur, R. Ophir, and D. Pelleg Constructing phylogenies from quartets: elucidation of eutherian superordinal relationships J. Comput. Biol. 5 3 1998 377 390
    • (1998) J. Comput. Biol. , vol.5 , Issue.3 , pp. 377-390
    • Ben-Dor, A.1    Chor, B.2    Graur, D.3    Ophir, R.4    Pelleg, D.5
  • 5
    • 0001117764 scopus 로고    scopus 로고
    • Inferring evolutionary trees with strong combinatorial evidence
    • V. Berry, and O. Gascuel Inferring evolutionary trees with strong combinatorial evidence Theor. Comput. Sci. 240 2 2000 271 298
    • (2000) Theor. Comput. Sci. , vol.240 , Issue.2 , pp. 271-298
    • Berry, V.1    Gascuel, O.2
  • 6
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • F. Hodson D. Kendall P. Tǎutu The Royal Society of London and The Academy of the Socialist Republic of Romania, the University Press, Edinburgh, pp. 387-395.
    • P. Buneman The recovery of trees from measures of dissimilarity F. Hodson D. Kendall P. Tǎutu Proceedings of the Anglo-Romanian conference The Royal Society of London and The Academy of the Socialist Republic of Romania, the University Press, Edinburgh, pp. 387-395. 1971
    • (1971) Proceedings of the Anglo-Romanian Conference
    • Buneman, P.1
  • 9
    • 0001978589 scopus 로고    scopus 로고
    • Analyzing and visualizing sequence and distance data using SPLITSTREE
    • A. Dress, D. Huson, and V. Moulton Analyzing and visualizing sequence and distance data using SPLITSTREE Discrete Appl. Math. 71 1-3 1996 95 109
    • (1996) Discrete Appl. Math. , vol.71 , Issue.1-3 , pp. 95-109
    • Dress, A.1    Huson, D.2    Moulton, V.3
  • 11
    • 0000347966 scopus 로고
    • Methods for computing Wagner trees
    • J. Farris Methods for computing Wagner trees Syst. Zool. 34 1970 21 24
    • (1970) Syst. Zool. , vol.34 , pp. 21-24
    • Farris, J.1
  • 12
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • J. Felsenstein Evolutionary trees from DNA sequences: a maximum likelihood approach J. Mol. Evol. 1981 368 376
    • (1981) J. Mol. Evol. , pp. 368-376
    • Felsenstein, J.1
  • 13
    • 0003437299 scopus 로고
    • Distributed by the author, Department of Genetics, University of Washington, Seattle
    • Felsenstein, J., 1993. Phylip (phylogeny inference package) version 3.5c. Distributed by the author, Department of Genetics, University of Washington, Seattle.
    • (1993) Phylip (Phylogeny Inference Package) Version 3.5c
    • Felsenstein, J.1
  • 14
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • W.M. Fitch Toward defining the course of evolution: minimum change for a specific tree topology Systematic Zoology 20 1971 406 416
    • (1971) Systematic Zoology , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 15
    • 0031678692 scopus 로고    scopus 로고
    • Splitstree: A program for analyzing and visualizing evolutionary data
    • D.H. Huson Splitstree: a program for analyzing and visualizing evolutionary data Bioinformatics 14 1 1998 68 73
    • (1998) Bioinformatics , vol.14 , Issue.1 , pp. 68-73
    • Huson, D.H.1
  • 17
    • 0033085036 scopus 로고    scopus 로고
    • Mammalian evolution: Timing and implications from using the logdeterminant transform for proteins of differing amino acid composition
    • D. Penny, M. Hasegawa, P.J. Waddell, and M.D. Hendy Mammalian evolution: timing and implications from using the logdeterminant transform for proteins of differing amino acid composition Syst. Biol. 48 1 1999 76 93
    • (1999) Syst. Biol. , vol.48 , Issue.1 , pp. 76-93
    • Penny, D.1    Hasegawa, M.2    Waddell, P.J.3    Hendy, M.D.4
  • 19
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • N. Saitou, and M. Nei The neighbor-joining method: a new method for reconstructing phylogenetic trees Mol. Biol. Evol. 4 1987 406 425
    • (1987) Mol. Biol. Evol. , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 21
    • 0036205377 scopus 로고    scopus 로고
    • TREE-PUZZLE: Maximum likelihood phylogenetic analysis using quartets and parallel computing
    • H.A. Schmidt, K. Strimmer, M. Vingron, and A. von Haeseler TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 2002 502 504
    • (2002) Bioinformatics , vol.18 , pp. 502-504
    • Schmidt, H.A.1    Strimmer, K.2    Vingron, M.3    Von Haeseler, A.4
  • 23
    • 52449147252 scopus 로고
    • The complexity of reconstructing trees from qualitive characters and subtrees
    • M. Steel The complexity of reconstructing trees from qualitive characters and subtrees J. Classification 9 1992 91 116
    • (1992) J. Classification , vol.9 , pp. 91-116
    • Steel, M.1
  • 24
  • 25
    • 0029836454 scopus 로고    scopus 로고
    • Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies
    • K. Strimmer, and A. von Haeseler Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies Mol. Biol. Evol. 13 7 1996 964 969
    • (1996) Mol. Biol. Evol. , vol.13 , Issue.7 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 26
    • 0027968068 scopus 로고
    • Clustal W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • J. Thompson, D. Higgins, and T. Gibson Clustal W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice Nucl. Acids Res. 22 1994 4673 4680
    • (1994) Nucl. Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.