Bayesian phylogeny on grid

Communications in Computer and Information Science

Volumn 13, Issue , 2008, Pages 404-416

  van der Wath, Richard C ^a   van der Wath, Elizabeth ^a   Carapelli, Antonio ^b   Nardi, Francesco ^b   Frati, Francesco ^b   Milanesi, Luciano ^c   Liò, Pietro ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF SIENA   (Italy)

^c INSTITUTE OF BIOMEDICAL TECHNOLOGIES   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIRDS; DNA SEQUENCES; SUPERCOMPUTERS;

APPROPRIATE MODELS; ARTHROPOD PHYLOGENY; BAYESIAN ALGORITHMS; CLUSTERS OF COMPUTERS; GRID INFRASTRUCTURES; LARGE DATASETS; PARALLEL SUPERCOMPUTING; PHYLOGENETIC INFERENCE;

GRID COMPUTING;

EID: 79954520395     PISSN: 18650929     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-70600-7_30     Document Type: Article

References (36)

1. Whelan, S., Lió, P., Goldman, N.: Molecular phylogenetics: State-of-art methods for looking into the past. Trends Genet. 17, 262-272 (2001)
2. Lió, P., Goldman, N.: Models of molecular evolution and phylogeny. Genome Res. 8, 1233-1244 (1998)
3. Carapelli, A., Lió, P., Nardi, F., van derWath, E., Frati, F.: Phylogenetic analysis of mitochondrial protein coding genes confirms the reciprocal paraphyly of Hexapoda and Crustacea. BMCEvolutionary Biology 7 (2007), doi:10.1186/1471-2148-7-S2-S8
4. Russo, C.A., Takezaki, N., Nei, M.: Efficiencies of different genes and different treebuilding methods in recovering a known vertebrate phylogeny. Mol. Biol. Evol. 13, 933-942 (1996)
5. Zardoya, R., Meyer, A.: Phylogenetic performance of mitochondrial protein-coding genes in resolving relationships among vertebrates. Molecular Biology and Evolution 13, 525-536 (1996)
6. Pollock, D.D., Eisen, J.A., Doggett, N.A., Cummings, M.P.: A case for the evolutionary genomics and the comprehensive examination of sequence biodiversity. Mol. Biol. Evol. 17, 1776-1778 (2000)
7. Cao, Y., Janke, A., Waddell, P.J., Westerman, M., Takenaka, O., Murata, S., Okada, N., Paabo, S., Hasegawa, M.: Conflict among individual mitochondrial proteins in resolving the phylogeny of eutherian orders. J. Mol. Evol. 47, 307-322 (1998)
8. Lió, P.: Phylogenetic and structural analysis of mitochondrial complex I proteins. Gene 345, 55-64 (1999)
9. Liu, J.S., Lawrence, C.E.: Bayesian inference on biopolymer models. Bioinformatics 15, 38-52 (1999)
10. Shoemaker, J.S., Painter, I.S., Weir, B.: Bayesian statistics in genetics: a guide for the uninitiated. Trends Genet. 15, 354-358 (1999)
11. Larget, B., Simon, D.: Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. E 16, 750-759 (1999)
12. Huelsenbeck, J.P., Ronquist, F.: MrBayes: Bayesian inference in phylogenetic trees. Bioinformatics 17, 754-755 (2001)
13. Ronquist, F., Huelsenbeck., J.P.: MrBayes3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574 (2003)
14. Rannala, B., Yang., Z.: Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics 164, 1645-1656 (2003)
15. Mau, B., Newton, M.A., Larget, B.: Bayesian phylogenetic inference via Markov chain Monte Carlo methods. Biometrics 55, 1-12 (1999)
16. Yang, Z., Rannala, B.: Bayesian phylogenetic inference using DNA sequences: Markov chain Monte Carlo methods. Mol. Biol. Evol. 14, 717-724 (1997)
17. Altekar, G., Dwarkadas, S., Huelsenbeck, J.P., Ronquist, F.: Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics 20, 407-415 (2004)
18. http://www.bioinfogrid.eu/
19. http://public.eu-egee.org/
20. Richter, S.: The Tetraconata concept: hexapod-crustacean relationships and the phylogeny of Crustacea. Org. Divers Evol. 2, 217-237 (2002)
21. Nardi, F., Spinsanti, G., Boore, J.L., Carapelli, A., Dallai, R., Frati, F.: Hexapod origins: monophyletic or polyphyletic? Science 299, 1887-1889 (2003)
22. Cook, C.E., Yue, Q., Akam, M.: Mitochondrial genomes suggest that hexapods and crustaceans are mutually paraphyletic. Proc. R Soc. Lond. B 272, 1295-1304 (2005)
23. Abascal, F., Posada, D., Zardoya, R.: MtArt: a new model of amino acid replacement for Arthropoda. Mol. Biol. Evol. 24, 1-5 (2007)
24. Yang, Z., Nielsen, R., Hasegawa: Models of amino acid substitutions and applications to mitochondrial protein evolution. Mol. Biol. Evol. 15, 1600-1611 (1998)
25. http://trinity.datamat.it/projects/EGEE/wiki/
26. http://public.eu-egee.org/industry/ifdocuments/glite-flyer.pdf
27. Boore, J.: Animal mitochondrial genomes. Nucl. Acid Res. 27, 1767-1780 (1999)
28. Cameron, S.L., Miller, K.B., DaHaese, C.A., Whiting, M.F., Barker, S.C.: Mitochondrial genome data alone are not enough to unambiguosly resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda). Cladistics 20, 534-557 (2004)
29. Hassanin, A., Lger, N., Deutsch, J.: Evidence for multiple reversals of asymmetric mutational constraints during the evolution of the mitochondrial genome of Metazoa, and consequences for phylogenetic inferences. Syt. Biol. 54, 277-298 (2005)
30. Chor, B., Hendy, M.D., Holland, B.R., Penny, D.: Multiple maxima of likelihood in phylogenetic trees: an analytic approach. In: RECOMB 2000, pp. 108-117 (2000)
31. Mossel, E., Vigoda, E.: Limitations of Markov chain Monte Carlo algorithms for Bayesian Inference of phylogeny. Ann. Appl. Probab. 16, 2215-2234 (2006)
32. Chor, B., Tuller, T.: Finding a maximum likelihood tree is hard. J. ACM 53, 722-744 (2006)
33. Gascuel, O.: Mathematics of Evolution and Phylogeny. Oxford University Press, USA (2007)
34. Yang, Z.: Computational Molecular Evolution (Oxford Series in Ecology and Evolution). Oxford University Press, USA (2006)
35. Felsenstein, J.: Inferring Phylogenies Sinauer Associates, 2nd edn (2003)
36. Nielsen, R.: Statistical Methods in Molecular Evolution (Statistics for Biology and Health), 1st edn. Springer, Heidelberg (2005)