메뉴 건너뛰기




Volumn 73, Issue 11, 2011, Pages 2627-2648

Optimality of the Neighbor Joining Algorithm and Faces of the Balanced Minimum Evolution Polytope

Author keywords

Balanced minimum evolution; Combinatorics; Neighbor joining; Phylogentic analysis; Polyhedral geometry

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; EVOLUTION; MATHEMATICAL PHENOMENA; PHYLOGENY;

EID: 81255142069     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-011-9640-x     Document Type: Article
Times cited : (27)

References (26)
  • 2
    • 34047267637 scopus 로고
    • A canonical decomposition theory for metrics on a finite set
    • Bandelt, H., & Dress, A. W. (1992). A canonical decomposition theory for metrics on a finite set. Adv. Math., 92, 47-105.
    • (1992) Adv. Math. , vol.92 , pp. 47-105
    • Bandelt, H.1    Dress, A.W.2
  • 4
    • 59649127986 scopus 로고    scopus 로고
    • Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference
    • Bordewich, M., Gascuel, O., Huber, K., & Moulton, V. (2009). Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 110-117.
    • (2009) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.6 , pp. 110-117
    • Bordewich, M.1    Gascuel, O.2    Huber, K.3    Moulton, V.4
  • 5
    • 23044465147 scopus 로고    scopus 로고
    • On the uniqueness of the selection criterion in neighbor-joining
    • Bryant, D. (2005). On the uniqueness of the selection criterion in neighbor-joining. J. Classif., 22, 3-15.
    • (2005) J. Classif. , vol.22 , pp. 3-15
    • Bryant, D.1
  • 6
    • 0002074731 scopus 로고
    • The recovery of trees from measures of similarity
    • F. Hodson, D. Kendall, and P. Tautu (Eds.), Edinburgh: Edinburgh University Press
    • Buneman, P. (1971). The recovery of trees from measures of similarity. In: F. Hodson, D. Kendall, & P. Tautu (Eds.), Mathematics of the archaeological and historical sciences (pp. 387-395). Edinburgh: Edinburgh University Press.
    • (1971) Mathematics of the Archaeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 9
    • 0023079987 scopus 로고
    • Computational complexity of inferring phylogenies from dissimilarity matrices
    • Day, W. (1987). Computational complexity of inferring phylogenies from dissimilarity matrices. Bull. Math. Biol., 49, 461-467.
    • (1987) Bull. Math. Biol. , vol.49 , pp. 461-467
    • Day, W.1
  • 10
    • 0026559592 scopus 로고
    • The consistency of several phylogeny-inference methods under varying evolutionary rates
    • DeBry, R. W. (1992). The consistency of several phylogeny-inference methods under varying evolutionary rates. Mol. Biol. Evol., 9, 537-551.
    • (1992) Mol. Biol. Evol. , vol.9 , pp. 537-551
    • Debry, R.W.1
  • 11
    • 0037375006 scopus 로고    scopus 로고
    • On the consistency of the minimum evolution principle of phylogenetic inference
    • Denis, F., & Gascuel, O. (2003). On the consistency of the minimum evolution principle of phylogenetic inference. Discrete Appl. Math., 127, 63-77.
    • (2003) Discrete Appl. Math. , vol.127 , pp. 63-77
    • Denis, F.1    Gascuel, O.2
  • 12
    • 0036943052 scopus 로고    scopus 로고
    • Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle
    • Desper, R., & Gascuel, O. (2002). Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol., 9(5), 687-705.
    • (2002) J. Comput. Biol. , vol.9 , Issue.5 , pp. 687-705
    • Desper, R.1    Gascuel, O.2
  • 13
    • 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
    • Desper, R., & Gascuel, O. (2004). Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol., 21, 587-598.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 587-598
    • Desper, R.1    Gascuel, O.2
  • 14
    • 45849084227 scopus 로고    scopus 로고
    • On the optimality of the neighbor-joining algorithm
    • URL
    • Eickmeyer, K., Huggins, P., Pachter, L., & Yoshida, R. (2008). On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol., 3(5). URL http://www. almob. org/content/3/1/5.
    • (2008) Algorithms Mol. Biol. , vol.3 , Issue.5
    • Eickmeyer, K.1    Huggins, P.2    Pachter, L.3    Yoshida, R.4
  • 16
    • 84959798530 scopus 로고
    • Cases in which parsimony and compatibility methods will be positively misleading
    • Felsenstein, J. (1978). Cases in which parsimony and compatibility methods will be positively misleading. Syst. Zool., 27, 401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 18
    • 33749540417 scopus 로고    scopus 로고
    • Neighbor-joining revealed
    • Gascuel, O., & Steel, M. (2006). Neighbor-joining revealed. Mol. Biol. Evol., 23, 1997-2000.
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 1997-2000
    • Gascuel, O.1    Steel, M.2
  • 19
    • 0033928038 scopus 로고    scopus 로고
    • Direct calculation of a tree length using a distance matrix
    • Pauplin, Y. (2000). Direct calculation of a tree length using a distance matrix. J. Mol. Evol., 51, 41-47.
    • (2000) J. Mol. Evol. , vol.51 , pp. 41-47
    • Pauplin, Y.1
  • 20
    • 33144459988 scopus 로고    scopus 로고
    • A short proof that phylogenetic tree reconstruction by maximum likelihood is hard
    • Roch, S. (2004). A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACM Trans. Comput. Biol. Bioinform., 3, 92-94.
    • (2004) IEEE/ACM Trans. Comput. Biol. Bioinform. , vol.3 , pp. 92-94
    • Roch, S.1
  • 21
    • 0023375195 scopus 로고
    • The neighbor joining method: a new method for reconstructing phylogenetic trees
    • Saitou, N., & 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
  • 23
    • 1642364229 scopus 로고    scopus 로고
    • Oxford lecture series in mathematics and its applications: Vol. 24
    • 0-19-850942-1, Oxford: Oxford University Press
    • Semple, C., & Steel, M. (2003). Oxford lecture series in mathematics and its applications: Vol. 24. Phylogenetics. Oxford: Oxford University Press. ISBN 0-19-850942-1.
    • (2003) Phylogenetics
    • Semple, C.1    Steel, M.2
  • 24
    • 12044252586 scopus 로고
    • Distributions of tree comparison metrics-some new results
    • Steel, M., & Penny, D. (1993). Distributions of tree comparison metrics-some new results. Syst. Biol., 42, 126-141.
    • (1993) Syst. Biol. , vol.42 , pp. 126-141
    • Steel, M.1    Penny, D.2
  • 25
    • 2442636143 scopus 로고    scopus 로고
    • Cyclic permutations and evolutionary trees
    • Steel, M., & Semple, C. (2004). Cyclic permutations and evolutionary trees. Adv. Appl. Math., 32, 669-680.
    • (2004) Adv. Appl. Math. , vol.32 , pp. 669-680
    • Steel, M.1    Semple, C.2
  • 26
    • 0024114801 scopus 로고
    • A note on the neighbor-joining method of Saitou and Nei
    • Studier, J. A., & Keppler, K. J. (1988). A note on the neighbor-joining method of Saitou and Nei. Mol. Biol. Evol., 5, 729-731.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.