Disk-covering, a fast-converging method for phylogenetic tree reconstruction

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 369-386

  Huson, Daniel H ^a   Nettles, Scott M ^b   Warnow, Tandy J ^c  

^a CELERA GENOMICS   (United States)

^b The University of Texas at Austin   (United States)

^c University of Texas at Austin ^*  (United States)

Author keywords

Algorithms; Biomolecular data; Chordal graphs; Clustering; Evolution; Jukes Cantor; Phylogenetic trees

Indexed keywords

CONFERENCE PAPER; GENE CONSTRUCT; GENE SEQUENCE; MATHEMATICAL MODEL; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY;

ALGORITHMS; BIOMETRY; EVALUATION STUDIES; MARKOV CHAINS; MODELS, STATISTICAL; PHYLOGENY;

EID: 0032746022     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318337     Document Type: Conference Paper

References (47)

1. Agarwala, R., Bafna, V., Farach, M., Narayanan, B., Paterson, M., and Thorup, M. 1996. On the approximability of numerical taxonomy: Fitting distances by tree metrics. Proc. 7th Annu. ACM-SIAM Symp. Discrete Algorithms 365-372.
2. Ambainis, R., Desper, R., Farach, M., and Kannan, S. 1997. Nearly tight bounds on the learnability of evolution. Proc. 38th Annu. IEEE Symp. Found. Comput. Sci. 524-533.
3. Atteson, K. 1997. The performance of neighbor-joining algorithms of phylogeny reconstruction, 101-110. In Jiang, T., and Lee, D., eds., Lecture Notes in Computer Science, 1276, Springer-Verlag, Berlin. COCOON '97.
4. Bandelt, H.-J., and Dress, A. 1992. A canonical decomposition theory for metrics on a finite set. Adv. Math. 92, 47-105.
5. Berry, V., and Gascuel, O. 1997. Inferring evolutionary trees with strong combinatorial evidence, 111-123. In Jiang, T., and Lee, D., eds., Lecture Notes in Computer Science, 1276, Springer-Verlag, Berlin. COCOON '97.
6. Buneman, P. 1971. The recovery of trees from measures of dissimilarity, 387-395. In Mathematics in the Archaeological and Historical Sciences, Edinburgh University Press, Edinburgh.
7. Buneman, P. 1974. A characterization of rigid circuit graphs. Discrete Math. 9, 205-212.
8. Cryan, M., Goldberg, L.A., and Goldberg, P.W. 1998. Evolutionary trees can be learned in polynomial time in the two-state general markov model. Proceedings of FOCS, 436-445.
9. Csuros, M., and Kao, M.-Y. 1999. Recovering evolutionary trees through harmonic greedy triplets. Proc. SODA'99, 261-268.
10. Day, W. 1995. Optimal algorithms for comparing trees with labelled leaves. J. Class. 2, 7-28.
11. Dobzhansky, T. 1993. Nothing in biology makes sense except in the light of evolution. Am. Biol. Teacher March, 125-129.
12. Erdos, P.L., Steel, M.A., Székely, L.A., and Warnow, T. 1997a. Constructing big trees from short sequences. In Goos, G., Hartmanis, J., and van Leeuwen, J., eds., Lecture Notes in Computer Science, volume 1256. ICALP'97, 827-837.
13. Erdos, P.L., Steel, M.A., Székely, L.Á., and Warnow, T. 1997b. A few logs suffice to build (almost) all trees II. Theor. Comp. Sci. 221, 77-118.
14. Erdos, PL., Steel, M.A., Székely, L.A., and Warnow, T. 1999. A few logs suffice to build (almost) all trees I. Random Struct. Algorithms 14(2), 153-184.
15. Farach, M., and Kannan, S. 1996. Efficient algorithms for inverting evolution. Proc. 28th Annu. ACM Symp. Theory Comput. J. ACM. In press;
16. STOC Proceedings, 230-236.
17. Farach, M., Kannan, S., and Warnow, T. 1995. A robust model for finding optimal evolutionary trees. Algorithmica 13(1), 155-179. (Special issue on Computational Biology.)
18. Felsenstein, J. 1988. Phylogenies from molecular sequences: Inference and reliability. Annu. Rev. Genet. 22, 521-565.
19. Golumbic, M. 1980. Algorithmic Graph Theory and Perfect Graphs. Academic Press, New York.
20. Gusfield, D. 1991. Efficient methods for multiple sequence alignment with guaranteed error bounds. Technical Report CSE 91-4, Computer Science Division, UC Davis.
21. Gusfield, D., and Wang, L. 1996. New uses for uniform lifted alignments. Technical Report CSE 96-4, Computer Science Division, UC Davis.
22. Hein, J. 1989. 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, 649-668.
23. Hillis, D. 1996. Inferring complex phylogenies. Nature (London) 383, 130-131.
24. Hillis, D., Huelsenbeck, J., and Cunningham, C. 1994. Application and accuracy of molecular phylogenies. Science 264, 671-677.
25. Huelsenbeck, J. 1995. Performance of phylogenetic methods in simulation. Syst. Biol. 44, 17-48.
26. Huelsenbeck, J., and Hillis, D. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42, 247-264.
27. Huson, D., Nettles, S., Parida, L., Warnow, T., and Yooseph, S., 1998a. The disk-covering method for tree reconstruction. Proc. "Algorithms and Experiments" (ALEX98), Trento 62-75.
28. Huson, D., Nettles, S., Rice, K., and Warnow, T. 1998b. Hybrid tree reconstruction methods. Proc. "Workshop Algorithm Engineer," Saarbrücken 172-192.
29. Jukes, T., and Cantor, C. 1969. Evolution of protein molecules, 21-132. In Munro, H., ed., Mammalian Protein Metabolism. Academic Press, New York.
30. Kuhner, M., and Felsenstein, J. 1994. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459-468.
31. Maddison, D.R., Ruvolo, M., and Swofford, D.L. 1992. Geographic origins of human mitochondrial DNA: Phylogenetic evidence from control region sequences. System. Zool. 41, 111-124.
32. McMorris, F., Warnow, T., and Wimer, T. 1994. Triangulating vertex-colored graphs. SIAM J. Discrete Math. 7(2), 296-306.
33. Phillips, C., and Warnow, T. 1996. The asymmetric median tree: A new model for building consensus trees. Discrete Appl. Math. 71, 311-335. (Special Issue on Computational Molecular Biology.)
34. Purvis, A., and Quicke, D. 1997. Building phylogenies: Are the big easy? Trends Ecol. Evol. 12(2), 49-50.
35. Rice, K. 1997. ECAT, an evolution simulator, http://www.cis.upenn.edu/~krice.
36. Rice, K., and Warnow, T. 1997. Parsimony is hard to beat!, 124-133. In Jiang, T., and Lee, D., eds., Lecture Notes in Computer Science, 1276, Springer-Verlag, Berlin. COCOON '97.
37. Rost, B., and Sander, C. 1993. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
38. Saitou, N., and Imanishi, T. 1989. 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, 514-525.
39. Saitou, N., and Nei, M. 1987. The neighbor-joining method: A new method, for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
40. Schöniger, M., and von Haeseler, A. 1995. Performance of maximum likelihood, neighbor-joining, and maximum parsimony methods when sequence sites are not independent. Syst. Biol. 44(4), 533-547.
41. Sourdis, J., and Nei, M. 1996. Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol. Biol. Evol. 5(3), 293-311.
42. Steel, M. 1992. The complexity of reconstructing trees from qualitative characters and subtrees. J. Class. 9, 91-116.
43. Steel, M.A., Székely, L.A., and Hendy, M.D. 1994. Reconstructing trees when sequence sites evolve at variable rate. J. Comput. Biol. 1(2), 153-163.
44. Strimmer, K., and von Haeseler, A. 1996. Accuracy of neighbor-joining for n-taxon trees. Syst. Biol. 45(4), 516-523.
45. Swofford, D.L., Olsen, G.J., Waddell, P.J., and Hillis, D.M. 1996. Phylogenetic inference, 407-514. In Hillis, D.M., Moritz, C., and Mable, B.K., eds., Molecular Systematics, 2nd ed. Sinauer, Sunderland, MA.
46. Warnow, T. 1996. Some combinatorial problems in phylogenetics. In Gýarfás, A., Lovász, L., and Székely, L.A., eds., Proceedings of Graph Theory and Combinatorial Biology, Balatonlelle, Hungary, July 15-20. Bolyai Soc. Math. Studies. 7, 363-413.
47. Waterman, M., Smith, T., and Beyer, W. 1977. Additive evolutionary trees. J. Theoret. Biol. 64, 199-213.