Large-scale phylogenetic reconstruction

Comparative Genomics: Basic and Applied Research

Volumn , Issue , 2007, Pages 29-48

  Moret, Bernard M E ^a  

^a EPFL   (Switzerland)

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EID: 67650330240     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1201/9781420008876     Document Type: Chapter

References (45)

1. M.G. Montague & C.A. Hutchinson III. Gene content and phylogeny of herpesviruses. Proceedings of the National Academy of Sciences of the United States of America, 97:5334-5339, 2000.
2. T. Dobzhansky. Nothing in biology makes sense except in the light of evolution. The American Biology Teacher, 35:125-129, 1973.
3. S. Yang, R. Doolittle & P. Bourne. Phylogeny determined by protein content. Proceedings of the National Academy of Sciences of the United States of America, 102(2):373-378, 2005.
4. B.M.E. Moret. Computational challenges from the tree of life. In Proc. 7th SIAM Workshop on Algorithm Engineering and Experiments (ALENEX’05), pp. 3-16, SIAM Press, Philadelphia, 2005.
5. K. Rice, M. Donoghue & R. Olmstead. Analyzing large datasets: rbcL500 revisited. Systematic Biology, 46:554-563, 1997.
6. T.F. Smith & M.S. Waterman. Identification of common molecular subsequences. Journal of Molecular Biology, 147:195-197, 1981.
7. D.A. Bader, B.M.E. Moret & M. Yan. A fast linear-time algorithm for inversion distance with an experimental comparison. Journal of Computational Biology, 8(5):483-491, 2001.
8. S. Hannenhalli & P.A. Pevzner. Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In Proceedings of the 27th Annual ACM Symposium on the Theory of Computing (STOC’95), pp. 178-189, ACM Press, New York, 1995.
9. S. Hannenhalli & P.A. Pevzner. Transforming mice into men (polynomial algorithm for genomic distance problems). In Proceedings of the 36th Annual IEEE Symposium on the Foundations of Computer Science (FOCS’95), pp. 581-592, IEEE Press, Piscataway, NJ, 4.
10. F.L. Swofford, G.J. Olsen, P.J. Waddell & D.M. Hillis. Phylogenetic inference. In D.M. Hillis, B.K. Mable, & C. Moritz, Eds., Molecular Systematics, pp. 407-514, Sinauer Associates, Sunderland, MA, 1996.
11. F.M.E. Moret, J. Tang, L.-S. Wang & T. Warnow. Steps toward accurate reconstructions of phylogenies from gene-order data. Journal of Computer Systems Science, 65(3):508-525, 2002.
12. N. Saitou & M. Nei. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4:406-425, 1987.
13. K. Atteson. The performance of the neighbor-joining methods of phylogenetic reconstruction. Algorithmica, 25(2-3):251-278, 1999.
14. E. Nakhleh, B.M.E. Moret, U. Roshan, K. St. John & T. Warnow. The accuracy of fast phylogenetic methods for large datasets. In Proceedings of the 7th Pacific Symposium on Biocomputing (PSB’02), pp. 211-222, World Scientific, 2002.
15. R. Daskalakis, C. Hill, A. Jaffe, R. Mihaescu, E. Mossel & S. Rao. Maximal accurate forests from distance matrices. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB’06), Vol. 3909 of Lecture Notes in Computer Science, pp. 281-295, Springer-Verlag, New York, 2006.
16. W.M. Fitch. On the problem of discovering the most parsimonious tree. American Naturalist, 111:223-257, 1977.
17. W.H.E. Day & D. Sankoff. Computational complexity of inferring phylogenies by compatibility. Systematic Zoology, 35(2):224-229, 1986.
18. P. Goloboff. Analyzing large datasets in reasonable times: solutions for composite optima. Cladistics, 15:415-428, 1999.
19. E.L. Williams, D.A. Bader, M. Yan & B.M.E. Moret. High-performance phylogeny reconstruction under maximum parsimony. In A.Y. Zomaya, Ed., Parallel Computing for Bioinformatics and Computational Biology, pp. 369-394, Wiley, New York, 2006.
20. S. Roch. A short proof that phylogenetic tree reconstruction by maximum likelihood is hard. ACM/IEEE Transactions on Computational Biology and Bioinformatics, 3(1), 2006.
21. D. Zwickl. GARLI. Available at www.zo.utexas.edu/faculty/antisense/Garli.html.
22. A. Stamatakis, T. Ludwig & H. Meier. RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21(4): 456-463, 2005.
23. E. Mossel & E. Vigoda. Limitations of Markov chain Monte Carlo algorithms for Bayesian inference of phylogeny [short report]. Science, 309(5744):2207-2209, 2005.
24. J.P. Huelsenbeck & F. Ronquist. MrBayes: Bayesian inference of phylogeny. Bioinformatics, 17:754b, 2001. Available at www.morphbank.ebc.uu.se/mrbayes/.
25. K. Strimmer & A. von Haeseler. Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13:964-969, 1996.
26. T. Warnow, B.M.E. Moret & K. St. John. Absolute convergence: true trees from short sequences. In Proc. 12th Annual ACM/SIAM Symposium on Discrete Algorithms (SODA’01), pp. 186-195, SIAM Press, 2001.
27. O.R.P. Bininda-Edmonds, Ed. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Kluwer Academic, Dordrecht, 2004.
28. F. Roshan, B.M.E. Moret, T. Warnow & T.L. Williams. Performance of supertree methods on various dataset decompositions. In O.R.P. Bininda-Edmonds, Ed., Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, pp. 301-328, Kluwer Academic, Dordrecht, 2004.
29. D. Huson, S. Nettles & T. Warnow. Disk-covering, a fast converging method for phylogenetic tree reconstruction. Journal of Compututational Biology, 6(3):369-386, 1999.
30. D. Huson, L. Vawter & T. Warnow. Solving large scale phylogenetic problems using DCM-2. In Proceedings of the 7th International Conference on Intelligent Systems for Molecular Biology (ISMB’99), pp. 118-129, AAAI Press, Menlo Park, CA, 1999.
31. U. Roshan, B.M.E. Moret, T.L. Williams & T. Warnow. Rec-I-DCM3: a fast algorithmic technique for reconstructing large phylogenetic trees. In Proceedings of the Third IEEE Computational Systems Bioinformatics Conference CSB’04, pp. 98-109, IEEE Press, Piscataway, NJ, 2004.
32. J. Tang & B.M.E. Moret. Scaling up accurate phylogenetic reconstruction from geneorder data. In Proc. 11th Int’l Conference on Intelligent Systems for Molecular Biology (ISMB’03), Vol. 19 of Bioinformatics, pp. i305-i312, Oxford University Press, New York, 2003.
33. D. Sankoff. Minimal mutation trees of sequences. SIAM Journal of Applied Mathematics, 28(1):35-42, 2004.
34. B.M.E. Moret, U. Roshan & T. Warnow. Sequence length requirements for phylogenetic methods. In Proceedings of the 2nd International Workshop on Algorithms in Bioinformatics (WABI’02), Vol. 2452 of Lecture Notes in Computer Science, pp. 343-356, Springer-Verlag, New York, 2002.
35. B.M.E. Moret, S.K. Wyman, D.A. Bader, T. Warnow & M. Yan. A new implementation and detailed study of breakpoint analysis. In Proceedings of the 6th Pacific Symposium on Biocomputing (PSB’01), pp. 583-594, World Scientific, 2001.
36. R.S. Johnson, G. Gutin, L.A. McGeoch, A. Yeo, W. Zhang & A. Zverovitch. Experimental analysis of heuristics for the ATSP. In G. Gutin & A.B. Punnen, Eds., The Traveling Salesman Problem and Its Variations, Vol. 12 of Combinatorial Optimization, pp. 445-487, Springer-Verlag, New York, 2002.
37. D.S. Johnson & L.A. McGeoch. The traveling salesman problem: a case study. In E. Aarts & J.K. Lenstra, Eds., Local Search in Combinatorial Optimization, pp. 215-310, Wiley, New York, 1997.
38. D.S. Johnson & L.A. McGeoch. Experimental analysis of heuristics for the STSP. In G. Gutin & A.B. Punnen, Eds., The Traveling Salesman Problem and Its Variations, Vol. 12 of Combinatorial Optimization, pp. 369-443, Springer-Verlag, New York, 2002.
39. E.R. Aragon, D.S. Johnson, L.A. McGeoch & C. Shevon. Optimization by simulated annealing: an experimental evaluation; part II, graph coloring and number partitioning. Operations Research, 39(3):378-406, 1991.
40. E.S. Johnson, C.R. Aragon, L.A. McGeoch & C.J. Shevon. Optimization by simulated annealing: an experimental evaluation; part I, graph partitioning. Operations Research, 37(6):865-892, 1989.
41. D. M. Hillis. Approaches for assessing phylogenetic accuracy. Systematic Biology, 44:3-16, 1995.
42. S.B. Heard. Patterns in phylogenetic tree balance with variable and evolving speciation rates. Evolution, 50:2141-2148, 1996.
43. A.O. Mooers & S.B. Heard. Inferring evolutionary process from phylogenetic tree shape. Quarterly Review of Biology, 72:31-54, 1997.
44. D.J. Aldous. Stochastic models and descriptive statistics for phylogenetic trees, from Yule to today. Statistical Science, 16:23-34, 2001.
45. E. Angelov, B. Harb, S. Kannan, S. Khanna & J. Kim. Efficient enumeration of phylogenetically informative substrings. In Proceedings of the 10th International Conference on Research in Computational Molecular Biology (RECOMB’06), Vol. 3909 of Lecture Notes in Computer Science, pp. 248-264, Springer-Verlag, New York, 2006.