Bootstrapping phylogenies inferred from rearrangement data

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 6833 LNBI, Issue , 2011, Pages 175-187

  Lin, Yu ^a   Rajan, Vaibhav ^a   Moret, Bernard M E ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

ASSESSMENT METHODS; COMPARATIVE GENOMICS; DATA SETS; DEGREE OF CONFIDENCE; DISTANCE-BASED; EVOLUTIONARY MODELS; EXPERIMENTAL TESTING; GENOMIC ARCHITECTURE; INFERENCE METHODS; MAMMALIAN GENOMES; MAXIMUM PARSIMONY; NON-PARAMETRIC; PHYLOGENETIC ANALYSIS; PHYLOGENETIC INFERENCE; PROBABILISTIC MODELS; RECEIVER OPERATING CHARACTERISTICS; SEARCH-BASED; SENSITIVITY AND SPECIFICITY; STANDARD METHOD; SUPPORT VALUE;

BIOINFORMATICS; EVOLUTIONARY ALGORITHMS; GENES; MAMMALS; MAXIMUM LIKELIHOOD; RATING; STATISTICAL TESTS;

INFERENCE ENGINES;

EID: 80053048032     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-23038-7_16     Document Type: Conference Paper

References (41)

1. Amrine-Madsen, H., Koepfli, K.P., Wayne, R., Springer, M.: A new phylogenetic marker, apolipoprotein b, provides compelling evidence for eutherian relationships. Mol. Phyl. Evol. 28(2), 225-240 (2003)
2. Anisimova, M., Gascuel, O.: Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst. Biol. 55(4), 539-552 (2006)
3. Bergeron, A., Mixtacki, J., Stoye, J.: A unifying view of genome rearrangements. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 163-173. Springer, Heidelberg (2006)
4. Cannarozzi, G., Schneider, A., Gonnet, G.: A phylogenomic study of human, dog, and mouse. PLoS Comput. Biol. 3, e2 (2007)
5. Desper, R., Gascuel, O.: Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21(3), 587-598 (2003)
6. Efron, B., Gong, G.: A leisurely look at the bootstrap, the jackknife, and cross-validation. American Statistician 37(1), 36-48 (1983)
7. Efron, B., Tibshirani, R., Tibshirani, R.: An Introduction to the Bootstrap. Chapman & Hall/CRC, Boca Raton (1993)
8. Farris, J.: The future of phylogeny reconstruction. Zoologica Scripta 26(4), 303-311 (1997)
9. Farris, J., Albert, V., Källersjö, M., Lipscomb, D., Kluge, A.: Parsimony jackknifing outperforms neighbor-joining. Cladistics 12(2), 99-124 (1996)
10. Felsenstein, J.: Confidence limits on phylogenies: an approach using the bootstrap. Evol. 39, 783-791 (1985)
11. Felsenstein, J., Kishino, H.: Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull. Syst. Biol. 42(2), 193-200 (1993)
12. Fertin, G., Labarre, A., Rusu, I., Tannier, E., Vialette, S.: Combinatorics of Genome Rearrangements. MIT Press, Cambridge (2009)
13. Guindon, S., Gascuel, O.: PHYML - a simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52(5), 696-704 (2003)
14. Hillis, D., Huelsenbeck, J.: Assessing molecular phylogenies. Science 267, 255-256 (1995)
15. Holmes, S.: Bootstrapping phylogenetic trees: theory and methods. Statistical Science 18(2), 241-255 (2003)
16. Hu, F., Gao, N., Tang, J.: Maximum likelihood phylogenetic reconstruction using gene order encodings. In: Proc. 8th IEEE Symp. Comput. Intell. in Bioinf. & Comput. Biol. (CIBCB 2011). IEEE Press, Los Alamitos (accepted, to appear 2011)
17. Huttley, G., Wakefield, M., Easteal, S.: Rates of genome evolution and branching order from whole-genome analysis. Mol. Biol. Evol. 24(8), 1722-1730 (2007)
18. Lin, Y., Moret, B.: Estimating true evolutionary distances under the DCJ model. In: Proc. 16th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB 2008) (2008); Bioinformatics 24(13), i114-i122 (2008)
19. Lin, Y., Rajan, V., Moret, B.: Fast and accurate phylogenetic reconstruction from high-resolution whole-genome data and a novel robustness estimator. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 137-148. Springer, Heidelberg (2010)
20. Lin, Y., Rajan, V., Swenson, K., Moret, B.: Estimating true evolutionary distances under rearrangements, duplications, and losses. In: Proc. 8th Asia Pacific Bioinf. Conf. (APBC 2010) (2010); BMC Bioinformatics 11(suppl. 1), s54 (2010)
21. Madsen, O., et al.: Parallel adaptive radiations in two major clades of placental mammals. Nature 409, 610-614 (2001)
22. Marron, M., Swenson, K., Moret, B.: Genomic distances under deletions and insertions. Theor. Comput. Sci. 325(3), 347-360 (2004)
23. Moret, B., Tang, J., Wang, L.S., Warnow, T.: Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65(3), 508-525 (2002)
24. Moret, B., Warnow, T.: Advances in phylogeny reconstruction from gene order and content data. In: Zimmer, E., Roalson, E. (eds.) Molecular Evolution: Producing the Biochemical Data, Part B. Methods in Enzymology, vol. 395, pp. 673-700. Elsevier, Amsterdam (2005)
25. Mort, M., Soltis, P., Soltis, D., Mabry, M.: Comparison of three methods for estimating internal support on phylogenetic trees. Syst. Biol. 49(1), 160-171 (2000)
26. Murphy, W., Eizirik, E., Johnson, W., Zhang, Y., Ryder, O., O'Brien, S.: Molecular phylogenetics and the origins of placental mammals. Nature 409, 614-618 (2001)
27. R Development Core Team: R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing (2009)
28. Rokas, A., Holland, P.: Rare genomic changes as a tool for phylogenetics. Trends in Ecol. and Evol. 15, 454-459 (2000)
29. Saitou, N., Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425 (1987)
30. Salamin, N., Chase, M., Hodkinson, T., Savolainen, V.: Assessing internal support with large phylogenetic DNA matrices. Mol. Phyl. Evol. 27(3), 528 (2003)
31. Shao, J., Wu, C.: A general theory for jackknife variance estimation. Annals of Statistics 17(3), 1176-1197 (1989)
32. Shi, J., Zhang, Y., Luo, H., Tang, J.: Using jackknife to assess the quality of gene order phylogenies. BMC Bioinformatics 11(1), 168 (2010)
33. Soltis, P., Soltis, D.: Applying the bootstrap in phylogeny reconstruction. Statist. Sci. 18(2), 256-267 (2003)
34. Swenson, K., Marron, M., Earnest-DeYoung, J., Moret, B.: Approximating the true evolutionary distance between two genomes. In: Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX 2005). SIAM Press, Philadelphia (2005)
35. Swofford, D., Olson, G., Waddell, P., Hillis, D.: Phylogenetic inference. In: Hillis, D., Moritz, C., Mable, B. (eds.) Molecular Systematics, 2nd edn., ch. 11. Sinauer Assoc. (1996)
36. Tannier, E.: Yeast ancestral genome reconstructions: The possibilities of computational methods. In: Ciccarelli, F.D., Miklós, I. (eds.) RECOMB-CG 2009. LNCS, vol. 5817, pp. 1-12. Springer, Heidelberg (2009)
37. Wang, L.S.: Exact-IEBP: a new technique for estimating evolutionary distances between whole genomes. In: Proc. 33rd Ann. ACM Symp. Theory of Comput. (STOC 2001), pp. 637-646. ACM Press, New York (2001)
38. Wang, L.S., Jansen, R., Moret, B., Raubeson, L., Warnow, T.: Fast phylogenetic methods for genome rearrangement evolution: An empirical study. In: Proc. 7th Pacific Symp. on Biocomputing (PSB 2002), pp. 524-535. World Scientific Pub., Singapore (2002)
39. Wang, L.S., Warnow, T.: Estimating true evolutionary distances between genomes. In: Gascuel, O., Moret, B.M.E. (eds.) WABI 2001. LNCS, vol. 2149, pp. 176-190. Springer, Heidelberg (2001)
40. Wildman, D., et al.: Genomics, biogeography, and the diversification of placental mammals. Proc. Nat'l. Acad. Sci., USA 104(36), 14395-14400 (2007)
41. Yancopoulos, S., Attie, O., Friedberg, R.: Efficient sorting of genomic permutations by translocation, inversion and block interchange. Bioinformatics 21(16), 3340-3346 (2005)