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Volumn 221, Issue 1-2, 1999, Pages 77-118

A few logs suffice to build (almost) all trees: Part II

Author keywords

Distance based methods; Dyadic closure method; Evolutionary tree reconstruction; Phylogeny; Quartet methods; Short quartet methods; Witness antiwitness method

Indexed keywords


EID: 0001860411     PISSN: 03043975     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0304-3975(99)00028-6     Document Type: Article
Times cited : (131)

References (64)
  • 5
    • 84947760192 scopus 로고    scopus 로고
    • The performance of neighbor-joining algorithms of phylogeny reconstruction
    • Computing and Combinatorics, 3rd Annual Internat. Conf., COCOON'97, Shanghai, China, August COCOON'97, Springer, Berlin
    • K. Atteson, The performance of neighbor-joining algorithms of phylogeny reconstruction, in: Computing and Combinatorics, 3rd Annual Internat. Conf., COCOON'97, Shanghai, China, August 1997, COCOON'97, Lecture Notes in Computer Science, vol. 1276, Springer, Berlin, pp. 101-110.
    • (1997) Lecture Notes in Computer Science , vol.1276 , pp. 101-110
    • Atteson, K.1
  • 6
    • 0000673494 scopus 로고
    • Reconstructing the shape of a tree from observed dissimilarity data
    • H.-J. Bandelt, A. Dress, Reconstructing the shape of a tree from observed dissimilarity data, Adv. Appl. Math. 7 (1986) 309-343.
    • (1986) Adv. Appl. Math. , vol.7 , pp. 309-343
    • Bandelt, H.-J.1    Dress, A.2
  • 7
    • 84947802748 scopus 로고    scopus 로고
    • Inferring evolutionary trees with strong combinatorial evidence
    • Computing and Combinatorics, 3rd Annual Internat. Conf., COCOON'97, Shanghai, China, August COCOON'97, Springer, Berlin
    • V. Berry, O. Gascuel, Inferring evolutionary trees with strong combinatorial evidence, in: Computing and Combinatorics, 3rd Annual Internat. Conf., COCOON'97, Shanghai, China, August 1997, COCOON'97, Lecture Notes in Computer Science, vol. 1276, Springer, Berlin, pp. 111-123.
    • (1997) Lecture Notes in Computer Science , vol.1276 , pp. 111-123
    • Berry, V.1    Gascuel, O.2
  • 8
    • 12044249534 scopus 로고
    • Probabilities of evolutionary trees
    • J.K.M. Brown, Probabilities of evolutionary trees, Syst. Biol. 43 (1994) 78-91.
    • (1994) Syst. Biol. , vol.43 , pp. 78-91
    • Brown, J.K.M.1
  • 9
    • 58149210897 scopus 로고
    • Extension operations on sets of leaf-labelled trees
    • D.J. Bryant, M.A. Steel, Extension operations on sets of leaf-labelled trees, Adv. Appl. Math. 16 (1995) 425-453.
    • (1995) Adv. Appl. Math. , vol.16 , pp. 425-453
    • Bryant, D.J.1    Steel, M.A.2
  • 10
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • F.R. Hodson, D.G. Kendall, P. Tautu (Eds.), Edinburgh University Press, Edinburgh
    • P. Buneman, The recovery of trees from measures of dissimilarity, in: F.R. Hodson, D.G. Kendall, P. Tautu (Eds.), Mathematics in the Archaeological and Historical Sciences, Edinburgh University Press, Edinburgh, 1971, pp. 387-395.
    • (1971) Mathematics in the Archaeological and Historical Sciences , pp. 387-395
    • Buneman, P.1
  • 12
    • 0018002532 scopus 로고
    • Taxonomy with confidence
    • J.A. Cavender, Taxonomy with confidence, Math. Biosci. 40 (1978) 271-280.
    • (1978) Math. Biosci. , vol.40 , pp. 271-280
    • Cavender, J.A.1
  • 16
    • 0032795125 scopus 로고    scopus 로고
    • Fast reconstruction of evolutionary trees through Harmonic Greedy Triplets
    • M. Csuros, M.-Y. Kao, Fast reconstruction of evolutionary trees through Harmonic Greedy Triplets, in: Proc. ACM-SIAM Symp. on Discrete Algorithms, 1999, pp. 261-268.
    • (1999) Proc. ACM-SIAM Symp. on Discrete Algorithms , pp. 261-268
    • Csuros, M.1    Kao, M.-Y.2
  • 17
    • 0040256028 scopus 로고
    • Computational complexity of inferring phylogenies from dissimilarities matrices
    • W.H.E. Day, Computational complexity of inferring phylogenies from dissimilarities matrices, Inform. Process. Lett. 30 (1989) 215-220.
    • (1989) Inform. Process. Lett. , vol.30 , pp. 215-220
    • Day, W.H.E.1
  • 18
    • 33845518635 scopus 로고    scopus 로고
    • Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule
    • P.L. Erdos, M.A. Steel, L.A. Székely, T. Warnow, Local quartet splits of a binary tree infer all quartet splits via one dyadic inference rule, Comput. Artif. Intell. 16 (2) (1997) 217-227.
    • (1997) Comput. Artif. Intell. , vol.16 , Issue.2 , pp. 217-227
    • Erdos, P.L.1    Steel, M.A.2    Székely, L.A.3    Warnow, T.4
  • 19
    • 0039664154 scopus 로고    scopus 로고
    • Inferring big trees from short quartets
    • ICALP'97, 24th Internat. Colloquium on Automata, Languages, and Programming, Silver Jubilee of EATCS, Bologna, Italy, July 7-11, 1997, Springer, Berlin
    • P.L. Erdos, M.A. Steel, L.A. Székely, T. Warnow, Inferring big trees from short quartets, in: ICALP'97, 24th Internat. Colloquium on Automata, Languages, and Programming, Silver Jubilee of EATCS, Bologna, Italy, July 7-11, 1997, Lecture Notes in Computer Science, vol. 1256, Springer, Berlin, 1997, pp. 1-11.
    • (1997) Lecture Notes in Computer Science , vol.1256 , pp. 1-11
    • Erdos, P.L.1    Steel, M.A.2    Székely, L.A.3    Warnow, T.4
  • 23
    • 0029192324 scopus 로고
    • A robust model for inferring optimal evolutionary trees
    • M. Farach, S. Kannan, T. Warnow, A robust model for inferring optimal evolutionary trees, Algorithmica 13 (1995) 155-179.
    • (1995) Algorithmica , vol.13 , pp. 155-179
    • Farach, M.1    Kannan, S.2    Warnow, T.3
  • 24
    • 84959807796 scopus 로고
    • A probability model for inferring evolutionary trees
    • J.S. Farris, A probability model for inferring evolutionary trees, Syst. Zool. 22 (1973) 250-256.
    • (1973) Syst. Zool. , vol.22 , pp. 250-256
    • Farris, J.S.1
  • 25
    • 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, Syst. Zool. 27 (1978) 401-410.
    • (1978) Syst. Zool. , vol.27 , pp. 401-410
    • Felsenstein, J.1
  • 26
    • 0000209031 scopus 로고
    • Numerical methods for inferring evolutionary trees
    • J. Felsenstein, Numerical methods for inferring evolutionary trees, Quart. Rev. Biol. 57 (1982) 379-404.
    • (1982) Quart. Rev. Biol. , vol.57 , pp. 379-404
    • Felsenstein, J.1
  • 27
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • D. Feng, R. Doolittle, Progressive sequence alignment as a prerequisite to correct phylogenetic trees, J. Mol. Evol. 25 (1987) 351-360.
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.1    Doolittle, R.2
  • 29
    • 0001996348 scopus 로고
    • The probabilities of rooted tree shapes generated by random bifurcation
    • E.F. Harding, The probabilities of rooted tree shapes generated by random bifurcation, Adv. Appl. Probab. 3 (1971) 44-77.
    • (1971) Adv. Appl. Probab. , vol.3 , pp. 44-77
    • Harding, E.F.1
  • 30
    • 0024766957 scopus 로고
    • A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given
    • J. Hein, A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given, Mol. Biol. Evol. 6 (1989) 649-668.
    • (1989) Mol. Biol. Evol. , vol.6 , pp. 649-668
    • Hein, J.1
  • 31
    • 11944260381 scopus 로고
    • Approaches for assessing phylogenetic accuracy
    • D. Hillis, Approaches for assessing phylogenetic accuracy, Syst. Biol. 44 (1995) 3-16.
    • (1995) Syst. Biol. , vol.44 , pp. 3-16
    • Hillis, D.1
  • 32
    • 0029834661 scopus 로고    scopus 로고
    • Inferring complex phylogenies
    • D. Hillis, Inferring complex phylogenies, Nature 383 (1996) 130-131.
    • (1996) Nature , vol.383 , pp. 130-131
    • Hillis, D.1
  • 33
    • 0021160693 scopus 로고
    • The alignment of sets of sequences and the construction of phylogenetic trees, an integrated method
    • P. Hogeweg, B. Hesper, The alignment of sets of sequences and the construction of phylogenetic trees, an integrated method, J. Mol. Evol. 20 (1984) 175-186.
    • (1984) J. Mol. Evol. , vol.20 , pp. 175-186
    • Hogeweg, P.1    Hesper, B.2
  • 34
    • 11944268967 scopus 로고
    • Performance of phylogenetic methods in simulation
    • J. Huelsenbeck, Performance of phylogenetic methods in simulation, Syst. Biol. 44 (1995) 17-48.
    • (1995) Syst. Biol. , vol.44 , pp. 17-48
    • Huelsenbeck, J.1
  • 35
    • 12044255023 scopus 로고
    • Success of phylogenetic methods in the four-taxon case
    • J.P. Huelsenbeck, D. Hillis, Success of phylogenetic methods in the four-taxon case, Syst. Biol. 42 (1993) 247-264.
    • (1993) Syst. Biol. , vol.42 , pp. 247-264
    • Huelsenbeck, J.P.1    Hillis, D.2
  • 36
    • 0348036777 scopus 로고    scopus 로고
    • Inferring very large evolutionary trees from very short sequences
    • D. Huson, S. Nettles, T. Warnow, Inferring very large evolutionary trees from very short sequences, Proc., RECOMB, 1999.
    • (1999) Proc., RECOMB
    • Huson, D.1    Nettles, S.2    Warnow, T.3
  • 38
    • 0346145079 scopus 로고    scopus 로고
    • personal communication
    • S. Kannan, personal communication.
    • Kannan, S.1
  • 39
    • 0001464973 scopus 로고
    • Estimation of evolutionary distances between homologous nucleotide sequences
    • M. Kimura, Estimation of evolutionary distances between homologous nucleotide sequences, Proc. Natl. Acad. Sci. USA 78 (1981) 454-458.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 454-458
    • Kimura, M.1
  • 40
    • 0001879933 scopus 로고
    • Molecular studies of evolution: A source of novel statistical problems
    • S.S. Gupta, J. Yackel (Eds.), Academic Press, New York
    • J. Neyman, Molecular studies of evolution: a source of novel statistical problems, in: S.S. Gupta, J. Yackel (Eds.), Statistical Decision Theory and Related Topics, Academic Press, New York, 1971, pp. 1-27.
    • (1971) Statistical Decision Theory and Related Topics , pp. 1-27
    • Neyman, J.1
  • 41
    • 0346145070 scopus 로고    scopus 로고
    • personal communication
    • K. Rice, personal communication.
    • Rice, K.1
  • 42
    • 84947793322 scopus 로고    scopus 로고
    • Parsimony is hard to beat
    • T. Jiang, D.T. Lee (Eds.), COCOON'97, Computing and Combinatorics, 3rd Annual Internat. Conf., Shanghai, August 20-22, Springer, Berlin
    • K. Rice, T. Wamow, Parsimony is hard to beat, in: T. Jiang, D.T. Lee (Eds.), COCOON'97, Computing and Combinatorics, 3rd Annual Internat. Conf., Shanghai, August 20-22, 1997, Lecture Notes in Computer Science, vol. 1276, Springer, Berlin, pp. 124-133.
    • (1997) Lecture Notes in Computer Science , vol.1276 , pp. 124-133
    • Rice, K.1    Wamow, T.2
  • 43
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • N. Saitou, 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
  • 44
    • 0000329594 scopus 로고
    • Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum likelihood, minimum evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree
    • N. Saitou, T. Imanishi, Relative efficiencies of the Fitch-Margoliash, maximum parsimony, maximum likelihood, minimum evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree, Mol. Biol. Evol. 6 (1987) 514-525.
    • (1987) Mol. Biol. Evol. , vol.6 , pp. 514-525
    • Saitou, N.1    Imanishi, T.2
  • 45
    • 0039574287 scopus 로고
    • A method for linear recording of graphs
    • Y.A. Smolensky, A method for linear recording of graphs, USSR Comput. Math. Phys. 2 (1969) 396-397.
    • (1969) USSR Comput. Math. Phys. , vol.2 , pp. 396-397
    • Smolensky, Y.A.1
  • 46
    • 52449147252 scopus 로고
    • The complexity of reconstructing trees from qualitative characters and subtrees
    • M.A. Steel, The complexity of reconstructing trees from qualitative characters and subtrees, J. Classification 9 (1992) 91-116.
    • (1992) J. Classification , vol.9 , pp. 91-116
    • Steel, M.A.1
  • 47
    • 43949153645 scopus 로고
    • Recovering a tree from the leaf colourations it generates under a Markov model
    • M.A. Steel, Recovering a tree from the leaf colourations it generates under a Markov model, Appl. Math. Lett. 7 (1994) 19-24.
    • (1994) Appl. Math. Lett. , vol.7 , pp. 19-24
    • Steel, M.A.1
  • 48
    • 0040843405 scopus 로고    scopus 로고
    • Reconstructing phylogenies from nucleotide pattern probabilities: A survey and some new results
    • M. Steel, M.D. Hendy, D. Penny, Reconstructing phylogenies from nucleotide pattern probabilities: a survey and some new results, Discrete Appl. Math. 89 (1999) 367-396.
    • (1999) Discrete Appl. Math. , vol.89 , pp. 367-396
    • Steel, M.1    Hendy, M.D.2    Penny, D.3
  • 49
    • 0028457461 scopus 로고
    • Reconstructing trees when sequence sites evolve at variable rates
    • M.A. Steel, L.A. Székely, M.D. Hendy, Reconstructing trees when sequence sites evolve at variable rates, J. Comput. Biol. 1 (1994) 153-163.
    • (1994) J. Comput. Biol. , vol.1 , pp. 153-163
    • Steel, M.A.1    Székely, L.A.2    Hendy, M.D.3
  • 50
    • 0029836454 scopus 로고    scopus 로고
    • Quartet Puzzling: A quartet Maximum Likelihood method for reconstructing tree topologies
    • K. Strimmer, A. von Haeseler, Quartet Puzzling: a quartet Maximum Likelihood method for reconstructing tree topologies, Mol. Biol. Evol. 13 (1996) 964-969.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 964-969
    • Strimmer, K.1    Von Haeseler, A.2
  • 52
    • 0001336205 scopus 로고    scopus 로고
    • Phylogenetic inference
    • Ch. 11, D.M. Hillis, C. Moritz, B.K. Mable (Eds.), Sinauer Associates, Inc., Sunderland
    • D.L. Swofford, G.J. Olsen, P.J. Waddell, D.M. Hillis, Phylogenetic inference, Ch. 11, in: D.M. Hillis, C. Moritz, B.K. Mable (Eds.), Molecular Systematics, 2nd ed., Sinauer Associates, Inc., Sunderland, 1996, pp. 407-514.
    • (1996) Molecular Systematics, 2nd Ed. , pp. 407-514
    • Swofford, D.L.1    Olsen, G.J.2    Waddell, P.J.3    Hillis, D.M.4
  • 53
    • 0021426157 scopus 로고
    • Fast algorithms for finding nearest common ancestors
    • D. Harel, R.E. Tarjan, Fast algorithms for finding nearest common ancestors, SIAM J. Comput. 13 (1984) 338-355.
    • (1984) SIAM J. Comput. , vol.13 , pp. 338-355
    • Harel, D.1    Tarjan, R.E.2
  • 54
    • 0028200719 scopus 로고
    • Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant
    • N. Takezaki, M. Nei, Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant, J. Mol. Evol. 39 (1994) 210-218.
    • (1994) J. Mol. Evol. , vol.39 , pp. 210-218
    • Takezaki, N.1    Nei, M.2
  • 55
    • 0022980133 scopus 로고
    • Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock
    • L. Vawter, W. Brown, Nuclear and mitochondrial DNA comparisons reveal extreme rate variation in the molecular clock, Science 234 (1986) 194-196.
    • (1986) Science , vol.234 , pp. 194-196
    • Vawter, L.1    Brown, W.2
  • 56
    • 0027309533 scopus 로고
    • Rates and patterns of base change in the small subunit ribosomal RNA gene
    • L. Vawter, W. Brown, Rates and patterns of base change in the small subunit ribosomal RNA gene, Genetics 134 (1993) 597-608.
    • (1993) Genetics , vol.134 , pp. 597-608
    • Vawter, L.1    Brown, W.2
  • 57
    • 0000503180 scopus 로고    scopus 로고
    • Improved approximation algorithms for tree alignment
    • L. Wang, D. Gusfield, Improved approximation algorithms for tree alignment, J. Algorithms 25 (1997) 255-273.
    • (1997) J. Algorithms , vol.25 , pp. 255-273
    • Wang, L.1    Gusfield, D.2
  • 58
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • L. Wang, T. Jiang, On the complexity of multiple sequence alignment, J. Comput. Biol. 1 (1994) 337-348.
    • (1994) J. Comput. Biol. , vol.1 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 59
    • 0000880429 scopus 로고    scopus 로고
    • Approximation algorithms for tree alignment with a given phylogeny
    • L. Wang, T. Jiang, E. Lawler, Approximation algorithms for tree alignment with a given phylogeny, Algorithmica 16 (1996) 302-315.
    • (1996) Algorithmica , vol.16 , pp. 302-315
    • Wang, L.1    Jiang, T.2    Lawler, E.3
  • 63
    • 0026563433 scopus 로고
    • The recent African genesis of humans
    • A.C. Wilson, R.L. Cann, The recent African genesis of humans, Scientific Amer. 266 (1992) 68-73.
    • (1992) Scientific Amer. , vol.266 , pp. 68-73
    • Wilson, A.C.1    Cann, R.L.2
  • 64
    • 0002275128 scopus 로고
    • Reconstruction of a tree from the distances between its pendant vertices
    • in Russian
    • K.A. Zaretsky, Reconstruction of a tree from the distances between its pendant vertices, Uspekhi Math. Nauk (Russian Mathematical Surveys) 20 (1965) 90-92 (in Russian).
    • (1965) Uspekhi Math. Nauk (Russian Mathematical Surveys) , vol.20 , pp. 90-92
    • Zaretsky, K.A.1


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