Efficient inference in phylogenetic InDel trees

Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference

Volumn , Issue , 2009, Pages 177-184

  Bouchard Côté, Alexandre ^a   Jordan, Michael I ^a,b   Klein, Dan ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CENTRAL PROBLEMS; COMPUTATIONAL BIOLOGY; COMPUTATIONAL PROBLEM; EVOLUTIONARY TREE; INDEPENDENCE ASSUMPTION; INSERTIONS AND DELETIONS; PHYLOGENETIC TREES; PHYLOGENETICS; PROBLEM DOMAIN; RESAMPLING;

PHYLOGENETIC;

EID: 84858779048     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (17)

1. N. Galtier, N. Tourasse, and M. Gouy. A nonhyperthermophilic common ancestor to extant life forms. Science, 283:220-221, 1999.
2. I. Holmes and W. J. Bruno. Evolutionary HMM: a Bayesian approach to multiple alignment. Bioinformatics, 17:803-820, 2001. (Pubitemid 32970479)
3. J. Felsenstein. Inferring Phylogenies. Sinauer Associates, 2003.
4. Z. Yang and B. Rannala. Bayesian phylogenetic inference using DNA sequences: A Markov chain Monte Carlo method. Molecular Biology and Evolultion, 14:717-724, 1997. (Pubitemid 27287292)
5. B. Mau and M. A. Newton. Phylogenetic inference for binary data on dendrograms using Markov chain Monte Carlo. Journal of Computational and Graphical Statistics, 6:122-131, 1997.
6. S. Li, D. K. Pearl, and H. Doss. Phylogenetic tree construction using Markov chain Monte Carlo. Journal of the American Statistical Association, 95:493-508, 2000.
7. W. J. Bruno, N. D. Socci, and A. L. Halpern. Weighted neighbor joining: A likelihoodbased approach to distance-based phylogeny reconstruction. Molecular Biology and Evolution, 17:189-197, 2000. (Pubitemid 30057004)
8. D. G. Higgins and P. M. Sharp. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene, 73:237-244, 1988. (Pubitemid 19033800)
9. J. L. Thorne, H. Kishino, and J. Felsenstein. Inching toward reality: an improved likelihood model of sequence evolution. Journal of Molecular Evolution, 34:3-16, 1992.
10. J. L. Thorne, H. Kishino, and J. Felsenstein. An evolutionary model for maximum likelihood alignment of DNA sequences. Journal of Molecular Evolution, 33:114-124, 1991.
11. G. A. Lunter, I. Miklós, Y. S. Song, and J. Hein. An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees. Journal of Computational Biology, 10:869-889, 2003. (Pubitemid 38156403)
12. A. Bouchard-Côté, P. Liang, D. Klein, and T. L. Griffiths. A probabilistic approach to diachronic phonology. In Proceedings of EMNLP 2007, 2007.
13. P. Diaconis, S. Holmes, and R. M. Neal. Analysis of a non-reversible Markov chain sampler. Technical report, Cornell University, 1997.
14. S. Needleman and C.Wunsch. A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology, 48:443-453, 1970.
15. K. St. John, T. Warnow, B. M. E. Moret, and L. Vawter. Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. Journal of Algorithms, 48:173-193, 2003.
16. J. Thompson, F. Plewniak, and O. Poch. BAliBASE: A benchmark alignments database for the evaluation of multiple sequence alignment programs. Bioinformatics, 15:87-88, 1999. (Pubitemid 29101202)
17. C. B. Do, M. S. P. Mahabhashyam, M. Brudno, and S. Batzoglou. PROBCONS: Probabilistic consistency-based multiple sequence alignment. Genome Research, 15:330-340, 2005. (Pubitemid 40309398)