Alignment-free phylogenetic reconstruction: Sample complexity via a branching process analysis

Annals of Applied Probability

Volumn 23, Issue 2, 2013, Pages 693-721

  Daskalakis, Constantinos ^a   Roch, Sebastien ^b  

^a Department of Electrical Engineering and Computer Science   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Alignment; Branching processes; Phylogenetic reconstruction

Indexed keywords

EID: 84879759464     PISSN: 10505164     EISSN: None     Source Type: Journal    
DOI: 10.1214/12-AAP852     Document Type: Article

References (42)

1. ANDONI, A., BRAVERMAN, M. and HASSIDIM, A. (2011). Phylogenetic reconstruction with insertions and deletions. Preprint.
2. ANDONI, A., DASKALAKIS, C., HASSIDIM, A. and ROCH, S. (2010). Global alignment of molecular sequences via ancestral state reconstruction. In ICS 2010 358-369. Tsinghua University Press, Beijing, China.
3. ATHREYA, K. B. and NEY, P. E. (1972). Branching Processes. Die Grundlehren der Mathematischen Wissenschaften 196. Springer, New York. MR0373040
4. ATTESON, K. (1999). The performance of neighbor-joining methods of phylogenetic reconstruction. Algorithmica 25 251-278. MR1703580
5. CSURÖS, M. (2002). Fast recovery of evolutionary trees with thousands of nodes. J. Comput. Biol. 9 277-297.
6. CSURÖS, M. and KAO, M.-Y. (2001). Provablyfastandaccuraterecoveryofevolutionarytrees through harmonic greedy triplets. SIAMJ. Comput. 31 306-322 (electronic). MR1857402
7. DASKALAKIS, C., HILL, C., JAFFE, A., MIHAESCU, R., MOSSEL, E. and RAO, S. (2006). Maximal accurate forests from distance matrices. In RECOMB 2006 281-295. Springer, Berlin.
8. DASKALAKIS, C., MOSSEL, E. and ROCH, S. (2006). Optimalphylogeneticreconstruction. In STOC'06: Proceedings of the 38th Annual ACM Symposium on Theory of Computing 159-168. ACM, New York. MR2277141
9. DASKALAKIS, C., MOSSEL, E. and ROCH, S. (2009). Phylogenies without branch bounds: Contracting the short, pruning the deep. In RECOMB 2009 451-465. Springer, Berlin.
10. DASKALAKIS, C. and ROCH, S. (2010). Alignment-free phylogenetic reconstruction. In RECOMB 2010 123-137. Springer, Berlin.
11. EDGAR, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 1792-1797.
12. ELIAS, I. (2006). Settling the intractability ofmultiple alignment. J. Comput. Biol. 13 1323-1339 (electronic). MR2264995
13. ERDÖS, P. L., STEEL, M. A., SZÉKELY, L. A. and WARNOW, T. J. (1999). A few logs suffice to build (almost) all trees. I. Random Structures Algorithms 14 153-184. MR1667319
14. ERDÖS, P. L., STEEL, M. A., SZÉKELY, L. A. and WARNOW, T. J. (1999). A few logs suffice to build (almost) all trees. II. Theoret. Comput. Sci. 221 77-118. MR1700821
15. FELSENSTEIN, J. (1978). Cases in which parsimony or compatibility methods will be positively misleading. Syst. Biol. 27 401-410.
16. FELSENSTEIN, J. (2004). Inferring Phylogenies. Sinauer, New York.
17. GRAUR, D. and LI, W. H. (1999). Fundamentals of Molecular Evolution, 2nd ed. Sinauer, Sunderland, MA.
18. GRONAU, I., MORAN, S. and SNIR, S. (2008). Fastandreliablereconstructionofphylogenetic trees with very short edges (extended abstract). In Proceedings of the Nineteenth Annual ACM-SIAMSymposium on Discrete Algorithms 379-388. ACM, New York. MR2487605
19. HIGGINS, D. G. and SHARP, P. M. (1988). Clustal: A package for performing multiple sequence alignment on a microcomputer. Gene 73 237-244.
20. HUSON, D. H., NETTLES, S. H. and WARNOW, T. J. (1999). Disk-covering, a fast-converging method for phylogenetic tree reconstruction. J. Comput. Biol. 6 3-4.
21. KARLIN, S. and TAYLOR, H. M. (1981). A Second Course in Stochastic Processes. Academic Press, New York. MR0611513
22. KATOH, K., MISAWA, K., KUMA, K.-I. and MIYATA, T. (2002). MAFFT: A novelmethod for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30 3059-3066.
23. KING, V., ZHANG, L. and ZHOU, Y (2003). On the complexity ofdistance-based evolutionary tree reconstruction. In Proceedings of the Fourteenth Annual ACM-SIAM Symposium on Discrete Algorithms (Baltimore, MD, 2003) 444-453. ACM, New York. MR1974948
24. LACEY, M. R. and CHANG, J. T. (2006). A signal-to-noise analysis ofphylogeny estimation by neighbor-joining: Insufficiency of polynomial length sequences. Math. Biosci. 199 188-215. MR2211625
25. LIU, K., RAGHAVAN, S., NELESEN, S., LINDER, C. R. and WARNOW, T. (2009). Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324 1561-1564.
26. LÖYTYNOJA, A. and GOLDMAN, N. (2008). Phylogeny-aware gap placementprevents errors in sequence alignment and evolutionary analysis. Science 320 1632-1635.
27. METZLER, D. (2003). Statistical alignment based on fragment insertion and deletion models. Bioinformatics 19 490-499.
28. MIKLOS, I., LUNTER, G. A. and HOLMES, I. (2004). A "Long Indel" model for evolutionary sequence alignment. Mol. Biol. Evol. 21 529-540.
29. MOSSEL, E. (2007). Distorted metrics on trees and phylogenetic forests. IEEE/ACM Trans. Comput. Bio. Bioinform. 4 108-116.
30. MOSSEL, E. and ROCH, S. (2006). Learning nonsingular phylogenies and hidden Markov models. Ann. Appl. Probab. 16 583-614. MR2244426
31. MOTWANI, R. and RAGHAVAN, P. (1995). Randomized Algorithms. Cambridge Univ. Press, Cambridge. MR1344451
32. RIVAS, E. and EDDY, S. R. (2008). Probabilistic phylogenetic inference with insertions and deletions. PLo S Comput. Biol. 4 e1000172, 20. MR2448496
33. ROCH, S. (2008). Sequence-length requirement for distance-based phylogeny reconstruction: Breaking the polynomial barrier. In FOCS 2008 729-738. IEEE Comput. Soc., Los Alamitos, CA.
34. SEMPLE, C. and STEEL, M. (2003). Phylogenetics. Oxford Lecture Series in Mathematics and Its Applications 24. Oxford Univ. Press, Oxford. MR2060009
35. STEEL, M. A. and SZÉKELY, L. A. (1999). Inverting random functions. Ann. Comb. 3 103-113. MR1769697
36. STEEL, M. A. and SZÉKELY, L. A. (2002). Inverting random functions. II. Explicit bounds for discrete maximum likelihood estimation, with applications. SIAM J. Discrete Math. 15 562-575 (electronic). MR1935839
37. SUCHARD, M. A. and REDELINGS, B. D. (2006). BAli-Phy: Simultaneous Bayesian inference of alignment and phylogeny. Bioinformatics 22 2047-2048.
38. THATTE, B. D. (2006). Invertibility of the TKF model of sequence evolution. Math. Biosci. 200 58-75. MR2211928
39. THORNE, J. L., KISHINO, H. and FELSENSTEIN, J. (1991). An evolutionary model for maximum likelihood alignment of dna sequences. Journal of Molecular Evolution 33 114-124.
40. THORNE, J. L., KISHINO, H. and FELSENSTEIN, J. (1992). Inching toward reality: An improved likelihood model of sequence evolution. Journal of Molecular Evolution 34 3-16.
41. WANG, L. and JIANG, T. (1994). On the complexity ofmultiple sequence alignment. J. Comput. Biol. 1 337-348.
42. WONG, K. M., SUCHARD, M. A. and HUELSENBECK, J. P. (2008). Alignment uncertainty and genomic analysis. Science 319 473-476. MR2381044