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Volumn 6044 LNBI, Issue , 2010, Pages 123-137

Alignment-free phylogenetic reconstruction

Author keywords

Alignment; Indels; Phylogenetic reconstruction

Indexed keywords

DISTANCE-BASED; INDELS; INSERTIONS AND DELETIONS; MULTIPLE ALIGNMENT; PHYLOGENETIC RECONSTRUCTION; POLYNOMIAL-TIME; SEQUENCE LENGTHS;

EID: 78650257028     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-12683-3_9     Document Type: Conference Paper
Times cited : (22)

References (41)
  • 1
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of dna sequences
    • Thorne, J.L., Kishino, H., Felsenstein, J.: An evolutionary model for maximum likelihood alignment of dna sequences. Journal of Molecular Evolution 33(2), 114-124 (1991).
    • (1991) Journal of Molecular Evolution , vol.33 , Issue.2 , pp. 114-124
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 2
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J.L., Kishino, H., Felsenstein, J.: Inching toward reality: An improved likelihood model of sequence evolution. Journal of Molecular Evolution 34(1), 3-16 (1992).
    • (1992) Journal of Molecular Evolution , vol.34 , Issue.1 , pp. 3-16
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 3
    • 46249095233 scopus 로고    scopus 로고
    • Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis
    • Loytynoja, A., Goldman, N.: Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis. Science 320(5883), 1632-1635 (2008).
    • (2008) Science , vol.320 , Issue.5883 , pp. 1632-1635
    • Loytynoja, A.1    Goldman, N.2
  • 4
    • 38549135938 scopus 로고    scopus 로고
    • Alignment uncertainty and genomic analysis
    • Wong, K.M., Suchard, M.A., Huelsenbeck, J.P.: Alignment Uncertainty and Genomic Analysis. Science 319(5862), 473-476 (2008).
    • (2008) Science , vol.319 , Issue.5862 , pp. 473-476
    • Wong, K.M.1    Suchard, M.A.2    Huelsenbeck, J.P.3
  • 5
    • 0037339432 scopus 로고    scopus 로고
    • Statistical alignment based on fragment insertion and deletion models
    • Metzler, D.: Statistical alignment based on fragment insertion and deletion models. Bioinformatics 19(4), 490-499 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 490-499
    • Metzler, D.1
  • 6
    • 1542510093 scopus 로고    scopus 로고
    • A "Long Indel" model for evolutionary sequence alignment
    • Miklos, I., Lunter, G.A., Holmes, I.: A "Long Indel" Model For Evolutionary Sequence Alignment. Mol. Biol. Evol. 21(3), 529-540 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , Issue.3 , pp. 529-540
    • Miklos, I.1    Lunter, G.A.2    Holmes, I.3
  • 7
    • 33747863926 scopus 로고    scopus 로고
    • BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny
    • Suchard, M.A., Redelings, B.D.: BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22(16), 2047-2048 (2006).
    • (2006) Bioinformatics , vol.22 , Issue.16 , pp. 2047-2048
    • Suchard, M.A.1    Redelings, B.D.2
  • 8
    • 52949150097 scopus 로고    scopus 로고
    • Probabilistic phylogenetic inference with insertions and deletions
    • Rivas, E., Eddy, S.R.: Probabilistic phylogenetic inference with insertions and deletions. PLoS Comput. Biol. 4, e1000172 (2008).
    • (2008) PLoS Comput. Biol. , vol.4
    • Rivas, E.1    Eddy, S.R.2
  • 9
    • 67649240664 scopus 로고    scopus 로고
    • Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    • Liu, K., Raghavan, S., Nelesen, S., Linder, C.R., Warnow, T.: Rapid and Accurate Large-Scale Coestimation of Sequence Alignments and Phylogenetic Trees. Science 324(5934), 1561-1564 (2009).
    • (2009) Science , vol.324 , Issue.5934 , pp. 1561-1564
    • Liu, K.1    Raghavan, S.2    Nelesen, S.3    Linder, C.R.4    Warnow, T.5
  • 10
    • 84959798530 scopus 로고
    • Cases in which parsimony or compatibility methods will be positively misleading
    • Felsenstein, J.: Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol., 401-410 (1978).
    • (1978) Syst. Biol. , pp. 401-410
    • Felsenstein, J.1
  • 15
    • 0001656793 scopus 로고    scopus 로고
    • The performance of neighbor-joining methods of phylogenetic reconstruction
    • Atteson, K.: 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
    • Atteson, K.1
  • 17
    • 0032746022 scopus 로고    scopus 로고
    • Disk-covering, a fast-converging method for phylogenetic tree reconstruction
    • Huson, D.H., Nettles, S.H., Warnow, T.J.: Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6(3-4) (1999).
    • (1999) J. Comput. Biol. , vol.6 , Issue.3-4
    • Huson, D.H.1    Nettles, S.H.2    Warnow, T.J.3
  • 18
    • 0011469880 scopus 로고    scopus 로고
    • Inverting random functions
    • Combinatorics and biology (Los Alamos, NM, 1998)
    • Steel, M.A., Székely, L.A.: Inverting random functions. Ann. Comb. 3(1), 103-113 (1999); Combinatorics and biology (Los Alamos, NM, 1998).
    • (1999) Ann. Comb. , vol.3 , Issue.1 , pp. 103-113
    • Steel, M.A.1    Székely, L.A.2
  • 19
    • 0036214723 scopus 로고    scopus 로고
    • Provably fast and accurate recovery of evolutionary trees through harmonic greedy triplets
    • Csurös, M., Kao, M.Y.: 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
  • 20
    • 0036108575 scopus 로고    scopus 로고
    • Fast recovery of evolutionary trees with thousands of nodes
    • Csurös, M.: Fast recovery of evolutionary trees with thousands of nodes. J. Comput. Biol. 9(2), 277-297 (2002).
    • (2002) J. Comput. Biol. , vol.9 , Issue.2 , pp. 277-297
    • Csurös, M.1
  • 21
    • 0036662360 scopus 로고    scopus 로고
    • Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications
    • (electronic)
    • Steel, M.A., Székely, L.A.: Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math. 15(4), 562-575 (2002) (electronic).
    • (2002) SIAM J. Discrete Math. , vol.15 , Issue.4 , pp. 562-575
    • Steel, M.A.1    Székely, L.A.2
  • 23
    • 33746918412 scopus 로고    scopus 로고
    • Learning nonsingular phylogenies and hidden Markov models
    • Mossel, E., Roch, S.: 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
  • 25
    • 32044432604 scopus 로고    scopus 로고
    • A signal-to-noise analysis of phylogeny estimation by neighborjoining: Insufficiency of polynomial length sequences
    • Lacey, M.R., Chang, J.T.: A signal-to-noise analysis of phylogeny estimation by neighborjoining: 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
    • 33745775198 scopus 로고    scopus 로고
    • Maximal accurate forests from distance matrices
    • Apostolico, A. Guerra, C. Istrail, S. Pevzner, P.A.Waterman, M. (eds.), LNCS (LNBI), Springer, Heidelberg
    • Daskalakis, C., Hill, C., Jaffe, A., Mihaescu, R., Mossel, E., Rao, S.: Maximal accurate forests from distance matrices. In: Apostolico, A., Guerra, C., Istrail, S., Pevzner, P.A., Waterman, M. (eds.) RECOMB 2006. LNCS (LNBI), vol. 3909, pp. 281-295. Springer, Heidelberg (2006).
    • (2006) RECOMB 2006 , vol.3909 , pp. 281-295
    • Daskalakis, C.1    Hill, C.2    Jaffe, A.3    Mihaescu, R.4    Mossel, E.5    Rao, S.6
  • 27
    • 33847726622 scopus 로고    scopus 로고
    • Distorted metrics on trees and phylogenetic forests
    • Mossel, E.: 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
  • 28
    • 58449096222 scopus 로고    scopus 로고
    • Fast and reliable reconstruction of phylogenetic trees with very short edges
    • Society for Industrial and Applied Mathematics, Philadelphia
    • Gronau, I., Moran, S., Snir, S.: Fast and reliable reconstruction of phylogenetic trees with very short edges. In: Proceedings of the nineteenth annual ACM-SIAM symposium on Discrete algorithms, pp. 379-388. Society for Industrial and Applied Mathematics, Philadelphia (2008).
    • (2008) Proceedings of the Nineteenth Annual ACM-SIAM Symposium on Discrete Algorithms , pp. 379-388
    • Gronau, I.1    Moran, S.2    Snir, S.3
  • 29
    • 57949099456 scopus 로고    scopus 로고
    • Sequence-length requirement for distance-based phylogeny reconstruction: Breaking the polynomial barrier
    • Roch, S.: Sequence-length requirement for distance-based phylogeny reconstruction: Breaking the polynomial barrier. In: FOCS, pp. 729-738 (2008).
    • (2008) FOCS , pp. 729-738
    • Roch, S.1
  • 30
    • 67650451289 scopus 로고    scopus 로고
    • Phylogenies without branch bounds: Contracting the short, pruning the deep
    • Batzoglou, S. (ed.), LNCS, Springer, Heidelberg
    • Daskalakis, C., Mossel, E., Roch, S.: Phylogenies without branch bounds: Contracting the short, pruning the deep. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 451-465. Springer, Heidelberg (2009).
    • (2009) RECOMB 2009 , vol.5541 , pp. 451-465
    • Daskalakis, C.1    Mossel, E.2    Roch, S.3
  • 31
    • 0028679709 scopus 로고
    • On the complexity of multiple sequence alignment
    • Wang, L., Jiang, T.: On the complexity of multiple sequence alignment. Journal of Computational Biology 1(4), 337-348 (1994).
    • (1994) Journal of Computational Biology , vol.1 , Issue.4 , pp. 337-348
    • Wang, L.1    Jiang, T.2
  • 32
    • 33846197539 scopus 로고    scopus 로고
    • Settling the intractability of multiple alignment
    • PMID: 17037961
    • Elias, I.: Settling the intractability of multiple alignment. Journal of Computational Biology 13(7), 1323-1339 (2006) PMID: 17037961.
    • (2006) Journal of Computational Biology , vol.13 , Issue.7 , pp. 1323-1339
    • Elias, I.1
  • 33
    • 0024234855 scopus 로고
    • Clustal: A package for performing multiple sequence alignment on a microcomputer
    • Higgins, D.G., Sharp, P.M.: Clustal: a package for performing multiple sequence alignment on a microcomputer. Gene 73(1), 237-244 (1988).
    • (1988) Gene , vol.73 , Issue.1 , pp. 237-244
    • Higgins, D.G.1    Sharp, P.M.2
  • 34
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Katoh, K., Misawa, K., Kuma, K.: MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucl. Acids Res. 30(14), 3059-3066 (2002).
    • (2002) Nucl. Acids Res. , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3
  • 35
    • 3042666256 scopus 로고    scopus 로고
    • MUSCLE: Multiple sequence alignment with high accuracy and high throughput
    • Edgar, R.C.: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl. Acids Res. 32(5), 1792-1797 (2004).
    • (2004) Nucl. Acids Res. , vol.32 , Issue.5 , pp. 1792-1797
    • Edgar, R.C.1
  • 36
    • 33644555241 scopus 로고    scopus 로고
    • Invertibility of the TKF model of sequence evolution
    • Thatte, B.D.: Invertibility of the TKF model of sequence evolution. Math. Biosci. 200(1), 58-75 (2006).
    • (2006) Math. Biosci. , vol.200 , Issue.1 , pp. 58-75
    • Thatte, B.D.1
  • 38
    • 34447260522 scopus 로고    scopus 로고
    • Is multiple-sequence alignment required for accurate inference of phylogeny?
    • Hohl, M., Ragan, M.A.: Is Multiple-Sequence Alignment Required for Accurate Inference of Phylogeny? Syst. Biol. 56(2), 206-221 (2007).
    • (2007) Syst. Biol. , vol.56 , Issue.2 , pp. 206-221
    • Hohl, M.1    Ragan, M.A.2
  • 39
    • 77955291662 scopus 로고
    • Academic Press Inc., [Harcourt Brace Jovanovich Publishers], New York
    • Karlin, S., Taylor, H.M.: A second course in stochastic processes, p. 542. Academic Press Inc.[Harcourt Brace Jovanovich Publishers], New York (1981).
    • (1981) A Second Course in Stochastic Processes , pp. 542
    • Karlin, S.1    Taylor, H.M.2
  • 40
    • 0002074731 scopus 로고
    • The recovery of trees from measures of dissimilarity
    • Edinburgh University Press, Edinburgh
    • Buneman, P.: The recovery of trees from measures of dissimilarity. In: Mathematics in the Archaelogical and Historical Sciences, pp. 187-395. Edinburgh University Press, Edinburgh (1971).
    • (1971) Mathematics in the Archaelogical and Historical Sciences , pp. 187-395
    • Buneman, P.1
  • 41
    • 0004217744 scopus 로고
    • Springer, New York; Die Grundlehren der mathematischen Wissenschaften, Band 196
    • Athreya, K.B., Ney, P.E.: Branching processes. Springer, New York (1972); Die Grundlehren der mathematischen Wissenschaften, Band 196.
    • (1972) Branching Processes
    • Athreya, K.B.1    Ney, P.E.2


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