메뉴 건너뛰기




Volumn 2, Issue 1, 2005, Pages 15-28

Topological rearrangements and local search method for tandem duplication trees

Author keywords

Local search; Minimum evolution; Parsimony; Phylogeny; Tandem duplication trees; Topological rearrangements; Zinc finger genes

Indexed keywords

ALGORITHMS; GENES; MATHEMATICAL MODELS; OPTIMIZATION; TREES (MATHEMATICS); ZINC;

EID: 19944393218     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2005.15     Document Type: Conference Paper
Times cited : (15)

References (55)
  • 2
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • E. Lander et al., "Initial Sequencing and Analysis of the Human Genome," Nature, vol. 409, pp. 860-921, 2001.
    • (2001) Nature , vol.409 , pp. 860-921
    • Lander, E.1
  • 3
    • 0032784908 scopus 로고    scopus 로고
    • Interspersed repeats and other mementos of transposable elements in mammalian genomes
    • A. Smit, "Interspersed Repeats and Other Mementos of Transposable Elements in Mammalian Genomes," Current Opinion in Genetics & Development, vol. 9, pp. 657-663, 1999.
    • (1999) Current Opinion in Genetics & Development , vol.9 , pp. 657-663
    • Smit, A.1
  • 4
    • 0017713284 scopus 로고
    • Phytogenies constrained by cross-over process as illustrated by human hemoglobins in a thirteen-cycle, eleven amino-acid repeat in human apolipoprotein A-I
    • W. Fitch, "Phytogenies Constrained by Cross-Over Process as Illustrated by Human Hemoglobins in a Thirteen-Cycle, Eleven Amino-Acid Repeat in Human Apolipoprotein A-I," Genetics, vol. 86, pp. 623-644, 1977.
    • (1977) Genetics , vol.86 , pp. 623-644
    • Fitch, W.1
  • 5
    • 0023256559 scopus 로고
    • Slipped-strand mispairing: A major mechanism for DNA sequence evolution
    • G. Levinson and G. Gutman, "Slipped-Strand Mispairing: A Major Mechanism for DNA Sequence Evolution," Molecular Biology and Evolution, vol. 4, pp. 203-221, 1987.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 203-221
    • Levinson, G.1    Gutman, G.2
  • 6
    • 0029671437 scopus 로고    scopus 로고
    • Evolution of antennapedia-class homeobox genes
    • J. Zhang and M. Nei, "Evolution of Antennapedia-Class Homeobox Genes," Genetics, vol. 142, no. 1, pp. 295-303, 1996.
    • (1996) Genetics , vol.142 , Issue.1 , pp. 295-303
    • Zhang, J.1    Nei, M.2
  • 8
    • 0036187352 scopus 로고    scopus 로고
    • Reconstructing the duplication history of tandemly repeated genes
    • O. Elemento, O. Gascuel, and M.-P. Lefranc, "Reconstructing the Duplication History of Tandemly Repeated Genes," Molecular Biology and Evolution, vol. 19, pp. 278-288, 2002.
    • (2002) Molecular Biology and Evolution , vol.19 , pp. 278-288
    • Elemento, O.1    Gascuel, O.2    Lefranc, M.-P.3
  • 10
    • 0036100845 scopus 로고    scopus 로고
    • Zinc finger gene clusters and tandem gene duplication
    • M. Tang, M. Waterman, and S. Yooseph, "Zinc Finger Gene Clusters and Tandem Gene Duplication," J. Computational Biology, vol. 9, pp. 429-446, 2002.
    • (2002) J. Computational Biology , vol.9 , pp. 429-446
    • Tang, M.1    Waterman, M.2    Yooseph, S.3
  • 11
    • 19944422932 scopus 로고    scopus 로고
    • A survey on algorithmic aspects of tandem repeats evolution
    • E. Rivals, "A Survey on Algorithmic Aspects of Tandem Repeats Evolution," Int'l J. Foundations of Computer Science, vol. 15, no. 2, pp. 225-257, 2004.
    • (2004) Int'l J. Foundations of Computer Science , vol.15 , Issue.2 , pp. 225-257
    • Rivals, E.1
  • 12
    • 19944418093 scopus 로고    scopus 로고
    • Reconstructing the duplication history of tandemly repeated sequences
    • O. Gascuel, ed.
    • O. Gascuel, D. Bertrand, and O. Elemento, "Reconstructing the Duplication History of Tandemly Repeated Sequences," Math. of Evolution and Phylogeny, O. Gascuel, ed., 2004.
    • (2004) Math. of Evolution and Phylogeny
    • Gascuel, O.1    Bertrand, D.2    Elemento, O.3
  • 15
    • 8444230206 scopus 로고    scopus 로고
    • Methods for reconstructing the history of tandem repeats and their application to the human genome
    • D. Jaitly, P. Kearney, G. Lin, and B. Ma, "Methods for Reconstructing the History of Tandem Repeats and Their Application to the Human Genome," J. Computer and System Sciences, vol. 65, pp. 494-507, 2002.
    • (2002) J. Computer and System Sciences , vol.65 , pp. 494-507
    • Jaitly, D.1    Kearney, P.2    Lin, G.3    Ma, B.4
  • 16
    • 0004069901 scopus 로고
    • San Francisco: W.H. Freeman and Company
    • P. Sneath and R. Sokal, Numerical Taxonomy, pp. 230-234, San Francisco: W.H. Freeman and Company, 1973.
    • (1973) Numerical Taxonomy , pp. 230-234
    • Sneath, P.1    Sokal, R.2
  • 17
    • 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," Molecular Biology and Evolution, vol. 4, pp. 406-425, 1987.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 18
    • 18544387648 scopus 로고    scopus 로고
    • A fast and accurate distance-based algorithm to reconstruct tandem duplication trees
    • O. Elemento and O. Gascuel, "A Fast and Accurate Distance-Based Algorithm to Reconstruct Tandem Duplication Trees," Bioinformatics, vol. 18, pp. 92-99, 2002.
    • (2002) Bioinformatics , vol.18 , pp. 92-99
    • Elemento, O.1    Gascuel, O.2
  • 20
    • 0000491446 scopus 로고
    • Additive similarity trees
    • S. Sattath and A. Tversky, "Additive Similarity Trees," Psychometrika, vol. 42, pp. 319-345, 1977.
    • (1977) Psychometrika , vol.42 , pp. 319-345
    • Sattath, S.1    Tversky, A.2
  • 21
    • 0041886965 scopus 로고    scopus 로고
    • Greedy method for inferring tandem duplication history
    • L. Zhang, B. Ma, L. Wang, and Y. Xu, "Greedy Method for Inferring Tandem Duplication History," Bioinformatics, vol. 19, pp. 1497-1504, 2003.
    • (2003) Bioinformatics , vol.19 , pp. 1497-1504
    • Zhang, L.1    Ma, B.2    Wang, L.3    Xu, Y.4
  • 24
    • 0000122573 scopus 로고
    • PHYLIP - PHYLogeny inference package
    • J. Felsenstein, "PHYLIP - PHYLogeny Inference Package," Cladistics, vol. 5, pp. 164-166, 1989.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 27
    • 2442717591 scopus 로고    scopus 로고
    • On counting tandem duplication trees
    • J. Yang and L. Zhang, "On Counting Tandem Duplication Trees," Molecular Biology and Evolution, vol. 21, pp. 1160-1163, 2004.
    • (2004) Molecular Biology and Evolution , vol.21 , pp. 1160-1163
    • Yang, J.1    Zhang, L.2
  • 28
    • 0003080472 scopus 로고
    • Comparison of labeled trees with valency trees
    • D. Robinson, "Comparison of Labeled Trees with Valency Trees," J. Combinatorial Theory, vol. 11, pp. 105-119, 1971.
    • (1971) J. Combinatorial Theory , vol.11 , pp. 105-119
    • Robinson, D.1
  • 29
    • 0000503180 scopus 로고    scopus 로고
    • Improved approximation algorithms for tree alignment
    • L. Wang and D. Gusfield, "Improved Approximation Algorithms for Tree Alignment," J. Algorithms, vol. 25, pp. 255-273, 1997.
    • (1997) J. Algorithms , vol.25 , pp. 255-273
    • Wang, L.1    Gusfield, D.2
  • 30
    • 0033928038 scopus 로고    scopus 로고
    • Direct calculation of a tree length using a distance matrix
    • Y. Pauplin, "Direct Calculation of a Tree Length Using a Distance Matrix," J. Molecular Evolution, vol. 51, pp. 41-47, 2000.
    • (2000) J. Molecular Evolution , vol.51 , pp. 41-47
    • Pauplin, Y.1
  • 31
    • 1542510099 scopus 로고    scopus 로고
    • Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting
    • R. Desper and O. Gascuel, "Theoretical Foundation of the Balanced Minimum Evolution Method of Phylogenetic Inference and Its Relationship to Weighted Least-Squares Tree Fitting," Molecular Biology and Evolution, vol. 21, no. 3, pp. 587-598, 2004.
    • (2004) Molecular Biology and Evolution , vol.21 , Issue.3 , pp. 587-598
    • Desper, R.1    Gascuel, O.2
  • 32
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specified tree topology
    • W. Fitch, "Toward Defining the Course of Evolution: Minimum Change for a Specified Tree Topology," Systematic Zoology, vol. 20, pp. 406-416, 1971.
    • (1971) Systematic Zoology , vol.20 , pp. 406-416
    • Fitch, W.1
  • 33
    • 0002329356 scopus 로고
    • Minimum mutation fits to a given tree
    • J. Hartigan, "Minimum Mutation Fits to a Given Tree," Biometrics, vol. 29, pp. 53-65, 1973.
    • (1973) Biometrics , vol.29 , pp. 53-65
    • Hartigan, J.1
  • 35
    • 0000621757 scopus 로고    scopus 로고
    • Methods for faster parsimony analysis
    • P.A. Goloboff, "Methods for Faster Parsimony Analysis," Cladistics, vol. 12, pp. 199-220, 1996.
    • (1996) Cladistics , vol.12 , pp. 199-220
    • Goloboff, P.A.1
  • 36
    • 0001117764 scopus 로고    scopus 로고
    • Inferring evolutionary trees with strong combinatorial evidence
    • V. Berry and O. Gascuel, "Inferring Evolutionary Trees with Strong Combinatorial Evidence," Theoretical Computer Science, vol. 240, pp. 271-298, 2000.
    • (2000) Theoretical Computer Science , vol.240 , pp. 271-298
    • Berry, V.1    Gascuel, O.2
  • 37
    • 0019296687 scopus 로고
    • A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • M. Kimura, "A Simple Model for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences," J. Molecular Evolution, vol. 16, pp. 111-120, 1980.
    • (1980) J. Molecular Evolution , vol.16 , pp. 111-120
    • Kimura, M.1
  • 38
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • D. Jones, W. Taylor, and J. Thornton, "The Rapid Generation of Mutation Data Matrices from Protein Sequences," Computer Applications in Biosciences, vol. 8, pp. 275-282, 1992.
    • (1992) Computer Applications in Biosciences , vol.8 , pp. 275-282
    • Jones, D.1    Taylor, W.2    Thornton, J.3
  • 39
    • 0015059567 scopus 로고
    • Phylogenetic analysis: Concepts and methods
    • K. Kidd and L. Sgaramella-Zonta, "Phylogenetic Analysis: Concepts and Methods," Am. J. Human Genetics, vol. 23, pp. 235-252, 1971.
    • (1971) Am. J. Human Genetics , vol.23 , pp. 235-252
    • Kidd, K.1    Sgaramella-Zonta, L.2
  • 40
    • 0027185401 scopus 로고
    • Theoretical foundation of the minimum-evolution method of phylogenetic inference
    • A. Rzhetsky and M. Nei, "Theoretical Foundation of the Minimum-Evolution Method of Phylogenetic Inference," Molecular Biology and Evolution, vol. 10, pp. 173-1095, 1993.
    • (1993) Molecular Biology and Evolution , vol.10 , pp. 173-1095
    • Rzhetsky, A.1    Nei, M.2
  • 41
    • 0023079987 scopus 로고
    • Computational complexity of inferring phylogenies from dissimilarity matrices
    • W. Day, "Computational Complexity of Inferring Phylogenies from Dissimilarity Matrices," Bull. Math. Biology, vol. 49, pp. 461-467, 1987.
    • (1987) Bull. Math. Biology , vol.49 , pp. 461-467
    • Day, W.1
  • 42
    • 2442636143 scopus 로고    scopus 로고
    • Cyclic permutations and evolutionary trees
    • C. Semple and M. Steel, "Cyclic Permutations and Evolutionary Trees," Advances in Applied Math., vol. 32, no. 4, pp. 669-680, 2004.
    • (2004) Advances in Applied Math. , vol.32 , Issue.4 , pp. 669-680
    • Semple, C.1    Steel, M.2
  • 43
    • 0036943052 scopus 로고    scopus 로고
    • Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
    • R. Desper and O. Gascuel, "Fast and Accurate Phylogeny Reconstruction Algorithms Based on the Minimum-Evolution Principle," J. Computational Biology, vol. 9, pp. 687-706, 2002.
    • (2002) J. Computational Biology , vol.9 , pp. 687-706
    • Desper, R.1    Gascuel, O.2
  • 44
    • 0028177080 scopus 로고
    • A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates
    • M. Kuhner and J. Felsenstein, "A Simulation Comparison of Phylogeny Algorithms under Equal and Unequal Evolutionary Rates," Molecular Biology and Evolution, vol. 11, pp. 459-468, 1994.
    • (1994) Molecular Biology and Evolution , vol.11 , pp. 459-468
    • Kuhner, M.1    Felsenstein, J.2
  • 45
    • 0030928378 scopus 로고    scopus 로고
    • Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • A. Rambault and N. Grassly, "Seq-Gen: An Application for the Monte Carlo Simulation of DNA Sequence Evolution Along Phylogenetic Trees," Computer Applied Biosciences, vol. 13, pp. 235-238, 1997.
    • (1997) Computer Applied Biosciences , vol.13 , pp. 235-238
    • Rambault, A.1    Grassly, N.2
  • 46
    • 0030034795 scopus 로고    scopus 로고
    • A hidden Markov model approach to variation among sites in rate of evolution
    • J. Felsenstein and G. Churchill, "A Hidden Markov Model Approach to Variation Among Sites in Rate of Evolution," Molecular Biology and Evolution, vol. 13, pp. 93-104, 1996.
    • (1996) Molecular Biology and Evolution , vol.13 , pp. 93-104
    • Felsenstein, J.1    Churchill, G.2
  • 48
    • 0026068337 scopus 로고
    • Zinc finger proteins: What we know and what we would like to know
    • T. El-Barabi and T. Pieler, "Zinc Finger Proteins: What We Know and What We Would Like to Know," Mechanisms of Development, vol. 33, pp. 155-169, 1991.
    • (1991) Mechanisms of Development , vol.33 , pp. 155-169
    • El-Barabi, T.1    Pieler, T.2
  • 50
    • 0031297695 scopus 로고    scopus 로고
    • General time reversible distances with unequal rates across sites: Mixing T and inverse Gaussian distributions with invariant sites
    • P. Waddel and M. Steel, "General Time Reversible Distances with Unequal Rates Across Sites: Mixing T and Inverse Gaussian Distributions with Invariant Sites," Molecular Phylogeny and Evolution, vol. 8, pp. 398-414, 1997.
    • (1997) Molecular Phylogeny and Evolution , vol.8 , pp. 398-414
    • Waddel, P.1    Steel, M.2
  • 51
    • 0033504552 scopus 로고    scopus 로고
    • The parsimony ratchet, a new method for rapid parsimony analysis
    • K.C. Nixon, "The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis," Cladistics, vol. 15, pp. 407-414, 1999.
    • (1999) Cladistics , vol.15 , pp. 407-414
    • Nixon, K.C.1
  • 52
    • 0242578620 scopus 로고    scopus 로고
    • A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood
    • S. Guindon and O. Gascuel, "A Simple, Fast and Accurate Method to Estimate Large Phylogenies by Maximum-Likelihood," Systematic Biology, vol. 52, no. 5, pp. 696-704, 2003.
    • (2003) Systematic Biology , vol.52 , Issue.5 , pp. 696-704
    • Guindon, S.1    Gascuel, O.2
  • 53
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • J. Felsenstein, "Cases in Which Parsimony or Compatibility Methods Will Be Positively Misleading," Systematic Zoology, vol. 27, pp. 401-410, 1978.
    • (1978) Systematic Zoology , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 54
    • 0031110886 scopus 로고    scopus 로고
    • From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem
    • D. Page and M. Charleston, "From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem," Molecular Phylogenetics and Evolution, vol. 7, pp. 231-240, 1997.
    • (1997) Molecular Phylogenetics and Evolution , vol.7 , pp. 231-240
    • Page, D.1    Charleston, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.