메뉴 건너뛰기




Volumn , Issue , 2008, Pages 729-738

Sequence length requirement of distance-based phylogeny reconstruction: Breaking the polynomial barrier

Author keywords

[No Author keywords available]

Indexed keywords

BRANCH LENGTHS; CONVENTIONAL WISDOMS; EVOLUTIONARY DISTANCES; LINEAR COMBINATIONS; MOLECULAR CLOCKS; PARAMETER SPACES; PHYLOGENY RECONSTRUCTIONS; PHYTOGENIES; SEQUENCE LENGTHS;

EID: 57949099456     PISSN: 02725428     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/FOCS.2008.77     Document Type: Conference Paper
Times cited : (15)

References (42)
  • 1
    • 0001656793 scopus 로고    scopus 로고
    • The performance of neighbor-joining methods of phylogenetic reconstruction
    • K Arteson. The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25(2-3):251-278, 1999.
    • (1999) Algorithmica , vol.25 , Issue.2-3 , pp. 251-278
    • Arteson, K.1
  • 2
    • 84972510219 scopus 로고
    • Statistical analysis of hominoid molecular evolution
    • With comments by Stephen Portnoy and Joseph Felsenstein and a reply by the authors
    • D. Barry and J. A. Hartigan. Statistical analysis of hominoid molecular evolution. Statist. Sci., 2(2): 191-210, 1987. With comments by Stephen Portnoy and Joseph Felsenstein and a reply by the authors.
    • (1987) Statist. Sci , vol.2 , Issue.2 , pp. 191-210
    • Barry, D.1    Hartigan, J.A.2
  • 3
    • 0030588055 scopus 로고    scopus 로고
    • Full reconstruction of Markov models on evolutionary trees: Identifiability and consistency
    • J. T. Chang. Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. Math. Biosci., 137(1):51-73, 1996.
    • (1996) Math. Biosci , vol.137 , Issue.1 , pp. 51-73
    • Chang, J.T.1
  • 5
    • 33845335476 scopus 로고    scopus 로고
    • Finding a maximum likelihood tree is hard
    • B. Chor and T. Tuller. Finding a maximum likelihood tree is hard. J. ACM, 53(5):722-744, 2006.
    • (2006) J. ACM , vol.53 , Issue.5 , pp. 722-744
    • Chor, B.1    Tuller, T.2
  • 6
    • 0036253383 scopus 로고    scopus 로고
    • M. Cryan, L. A. Goldberg, and P. W. Goldberg. Evolutionary trees can be learned in polynomial time. SIAM J. Comput., 31(2):375-397, 2002. short version, Proceedings of the 39th Annual Symposium on Foundations of Computer Science (FOCS 98), pages 436-445, 1998.
    • M. Cryan, L. A. Goldberg, and P. W. Goldberg. Evolutionary trees can be learned in polynomial time. SIAM J. Comput., 31(2):375-397, 2002. short version, Proceedings of the 39th Annual Symposium on Foundations of Computer Science (FOCS 98), pages 436-445, 1998.
  • 7
    • 0036108575 scopus 로고    scopus 로고
    • Fast recovery of evolutionary trees with thousands of nodes
    • M. Csurös. Fast recovery of evolutionary trees with thousands of nodes. J. Comput Biol., 9(2):277-97, 2002.
    • (2002) J. Comput Biol , vol.9 , Issue.2 , pp. 277-297
    • Csurös, M.1
  • 8
    • 0036214723 scopus 로고    scopus 로고
    • Provably fast and accurate recovery of evolutionary trees through harmonic greedy triplets
    • M. Csurös and M.-Y. Kao. Provably fast and accurate recovery of evolutionary trees through harmonic greedy triplets. SIAM Journal on Computing, 31(1):306-322, 2001.
    • (2001) SIAM Journal on Computing , vol.31 , Issue.1 , pp. 306-322
    • Csurös, M.1    Kao, M.-Y.2
  • 11
    • 57949091019 scopus 로고    scopus 로고
    • Evolutionaty trees and the Ising model on the Bethe lattice: A proof of Steel's conjecture
    • Preprint
    • C. Daskalakis, E. Mossel, and S. Roch. Evolutionaty trees and the Ising model on the Bethe lattice: a proof of Steel's conjecture. Preprint, 2008.
    • (2008)
    • Daskalakis, C.1    Mossel, E.2    Roch, S.3
  • 12
    • 57949090519 scopus 로고    scopus 로고
    • Phylogenies without branch bounds: Contracting the short, pruning the deep
    • Preprint
    • C. Daskalakis, E. Mossel, and S. Roch. Phylogenies without branch bounds: Contracting the short, pruning the deep. Preprint, 2008.
    • (2008)
    • Daskalakis, C.1    Mossel, E.2    Roch, S.3
  • 13
    • 0023079987 scopus 로고
    • Computational complexity of inferring phylogenies from dissimilarity matrices
    • W. H. E. Day. Computational complexity of inferring phylogenies from dissimilarity matrices. Bull. Math. Biol., 49(4):461-467, 1987.
    • (1987) Bull. Math. Biol , vol.49 , Issue.4 , pp. 461-467
    • Day, W.H.E.1
  • 14
    • 0004485904 scopus 로고
    • Computational complexity of inferring phylogenies by compatibility
    • W. H. E. Day and D. Sankoff. Computational complexity of inferring phylogenies by compatibility. Syst. Zool., 35(2):224-229, 1986.
    • (1986) Syst. Zool , vol.35 , Issue.2 , pp. 224-229
    • Day, W.H.E.1    Sankoff, D.2
  • 16
    • 0001860411 scopus 로고    scopus 로고
    • P. L. Erdös, M. A. Steel, L. A. Székely, and T. A. Warnow. A. few logs suffice to build (almost) all trees (part 2). Theor. Comput Sci., 221:77-118, 1999.
    • P. L. Erdös, M. A. Steel, L. A. Székely, and T. A. Warnow. A. few logs suffice to build (almost) all trees (part 2). Theor. Comput Sci., 221:77-118, 1999.
  • 18
    • 0000161374 scopus 로고    scopus 로고
    • Efficient algorithms for inverting evolution
    • M. Farach and S. Kannan. Efficient algorithms for inverting evolution. J. ACM, 46(4):437-449, 1999.
    • (1999) J. ACM , vol.46 , Issue.4 , pp. 437-449
    • Farach, M.1    Kannan, S.2
  • 20
    • 0030807655 scopus 로고    scopus 로고
    • BIO-NJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • O. Gascuel. BIO-NJ: An improved version of the NJ algorithm based on a simple model of sequence data. Mol. Biol. Evol., 14(7): 685-695, 1997.
    • (1997) Mol. Biol. Evol , vol.14 , Issue.7 , pp. 685-695
    • Gascuel, O.1
  • 22
    • 0020308198 scopus 로고
    • Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time
    • R. L. Graham., and L. R. Foulds. Unlikelihood that minimal phylogenies for a realistic biological study can be constructed in reasonable computational time. Math. Biosci., 60:133-142, 1982.
    • (1982) Math. Biosci , vol.60 , pp. 133-142
    • Graham, R.L.1    Foulds, L.R.2
  • 23
    • 57949110804 scopus 로고    scopus 로고
    • I. Gronau, S. Moran, and S. Snir. Fast and reliable reconstruction of phylogenetic trees with very short edges. To appear in SODA, 2008.
    • I. Gronau, S. Moran, and S. Snir. Fast and reliable reconstruction of phylogenetic trees with very short edges. To appear in SODA, 2008.
  • 24
    • 0038077526 scopus 로고    scopus 로고
    • On the complexity of distance-based evolutionary tree reconstruction
    • Philadelphia, PA, USA, Society for Industrial and Applied Mathematics
    • V. King, L. Zhang, and Y Zhou. On the complexity of distance-based evolutionary tree reconstruction. In SODA '03: Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms, pages 444-453, Philadelphia, PA, USA, 2003. Society for Industrial and Applied Mathematics.
    • (2003) SODA '03: Proceedings of the fourteenth annual ACM-SIAM symposium on Discrete algorithms , pp. 444-453
    • King, V.1    Zhang, L.2    Zhou, Y.3
  • 25
    • 32044432604 scopus 로고    scopus 로고
    • A signal-to-noise analysis of phylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences
    • M. R. Lacey and J. T. Chang. A signal-to-noise analysis of phylogeny estimation by neighbor-joining: insufficiency of polynomial length sequences. Math. Biosci., 199(2):188-215, 2006.
    • (2006) Math. Biosci , vol.199 , Issue.2 , pp. 188-215
    • Lacey, M.R.1    Chang, J.T.2
  • 26
    • 0028181246 scopus 로고
    • Reconstructing Evolutionary Trees from DNA and Protein Sequences: Paralinear Distances
    • J. Lake. Reconstructing Evolutionary Trees from DNA and Protein Sequences: Paralinear Distances. Proceedings of the National Academy of Sciences, 91(4):1455-1459, 1994.
    • (1994) Proceedings of the National Academy of Sciences , vol.91 , Issue.4 , pp. 1455-1459
    • Lake, J.1
  • 28
    • 0028361182 scopus 로고
    • Recovering Evolutionary Trees under a More Realistic Model of Sequence
    • P. Lockhart, M. Steel, M. Hendy, and D. Penny. Recovering Evolutionary Trees under a More Realistic Model of Sequence. Mol Biol Evol, 11(4):605-612, 1994.
    • (1994) Mol Biol Evol , vol.11 , Issue.4 , pp. 605-612
    • Lockhart, P.1    Steel, M.2    Hendy, M.3    Penny, D.4
  • 29
    • 0242523720 scopus 로고    scopus 로고
    • On the impossibility of reconstructing ancestral data and phylogenies
    • E. Mossel. On the impossibility of reconstructing ancestral data and phylogenies. J. Comput. Biol., 10(5):669-678, 2003.
    • (2003) J. Comput. Biol , vol.10 , Issue.5 , pp. 669-678
    • Mossel, E.1
  • 30
    • 2442663027 scopus 로고    scopus 로고
    • Phase transitions in phylogeny
    • E. Mossel. Phase transitions in phylogeny. Trans. Amer. Math. Soc., 356(6):2379-2404, 2004.
    • (2004) Trans. Amer. Math. Soc , vol.356 , Issue.6 , pp. 2379-2404
    • Mossel, E.1
  • 31
    • 33847726622 scopus 로고    scopus 로고
    • Distorted metrics on trees and phylogenetic forests
    • E. Mossel. Distorted metrics on trees and phylogenetic forests. IEEE/ACM Trans. Comput Bio. Bioinform., 4(1): 108-116, 2007.
    • (2007) IEEE/ACM Trans. Comput Bio. Bioinform , vol.4 , Issue.1 , pp. 108-116
    • Mossel, E.1
  • 32
    • 1842550501 scopus 로고    scopus 로고
    • Information flow on trees
    • E. Mossel and Y Peres. Information flow on trees. Ann. Appl. Probab., 13(3):817-844, 2003.
    • (2003) Ann. Appl. Probab , vol.13 , Issue.3 , pp. 817-844
    • Mossel, E.1    Peres, Y.2
  • 33
    • 33746918412 scopus 로고    scopus 로고
    • Learning nonsingular phylogenies and hidden Markov models
    • E. Mossel and S. Roch. Learning nonsingular phylogenies and hidden Markov models. Ann. Appl. Probab., 16(2):583-614, 2006.
    • (2006) Ann. Appl. Probab , vol.16 , Issue.2 , pp. 583-614
    • Mossel, E.1    Roch, S.2
  • 34
    • 25844516325 scopus 로고    scopus 로고
    • Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees
    • E. Mossel and E. Vigoda. Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees. Science, 309(5744):2207-2209, 2005.
    • (2005) Science , vol.309 , Issue.5744 , pp. 2207-2209
    • Mossel, E.1    Vigoda, E.2
  • 35
    • 33144459988 scopus 로고    scopus 로고
    • A short proof that phylogenetic tree reconstruction by maximum likelihood is hard
    • 92-94
    • S. Roch. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. IEEE/ACM Trans. Comput. Biology Bioinform., 3(1):92-94, 2006.
    • (2006) IEEE/ACM Trans. Comput. Biology Bioinform , vol.3 , Issue.1
    • Roch, S.1
  • 36
    • 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(4):406-425, 1987.
    • (1987) Mol. Biol. Evol , vol.4 , Issue.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 37
    • 0000491446 scopus 로고
    • Additive similarity trees
    • S. Sattath and A. Tversky. Additive similarity trees. Psychometrika, 42:319-345,1977.
    • (1977) Psychometrika , vol.42 , pp. 319-345
    • Sattath, S.1    Tversky, A.2
  • 39
    • 43949153645 scopus 로고
    • Recovering a tree from the leaf colourations it generates under a Markov model
    • M. Steel. Recovering a tree from the leaf colourations it generates under a Markov model. Appl. Math. Lett., 7(2): 19-23, 1994.
    • (1994) Appl. Math. Lett , vol.7 , Issue.2 , pp. 19-23
    • Steel, M.1
  • 40
    • 0345832906 scopus 로고    scopus 로고
    • My Favourite Conjecture
    • Preprint
    • M. Steel. My Favourite Conjecture. Preprint, 2001.
    • (2001)
    • Steel, M.1
  • 41
    • 0011469880 scopus 로고    scopus 로고
    • Inverting random functions
    • Combinatorics and biology Los Alamos, NM
    • M. A. Steel and L. A. Székely. Inverting random functions. Ann. Comb, 3(1): 103-113, 1999. Combinatorics and biology (Los Alamos, NM, 1998).
    • (1998) Ann. Comb , vol.3 , Issue.1 , pp. 103-113
    • Steel, M.A.1    Székely, L.A.2
  • 42
    • 0036662360 scopus 로고    scopus 로고
    • M. A. Steel and L. A. Székely. Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math., 15(4):562-575 (electronic), 2002.
    • M. A. Steel and L. A. Székely. Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math., 15(4):562-575 (electronic), 2002.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.