Reconstructing approximate phylogenetic trees from quartet samples

Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Volumn , Issue , 2010, Pages 1035-1044

  Snir, Sagi ^a   Yuster, Raphael ^a  

^a UNIVERSITY OF HAIFA   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS;

APPROXIMATION RATIOS; BIG TREES; EVOLUTIONARY TREE; MAXIMUM QUARTET CONSISTENCIES; PHYLOGENETIC RECONSTRUCTION; PHYLOGENETIC TREES; QUARTET BASED METHOD; RANDOM SAMPLE;

APPROXIMATION ALGORITHMS;

EID: 77951683418     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1137/1.9781611973075.84     Document Type: Conference Paper

References (15)

1. N. Alon and J. Spencer. The Probabilistic Method. John Wiley, 1992.
2. Constantinos Daskalakis, Cameron Hill, Alexander Jaffe, Radu Mihaescu, Elchanan Mossel, and Satish Rao. Maximal accurate forests from distance matrices. In RECOMB, pages 281-295, 2006.
3. Constantinos Daskalakis, Elchanan Mossel, and Sébastien Roch. Optimal phylogenetic reconstruction. In STOC, pages 159-168, 2006.
4. P. Erdocombining double acute accents, M. Steel, L. Szekely, and T. Warnow. A few logs suffice to build (almost) all trees (i). Random Structures and Algorithms, 14:153-184, 1999.
5. P. Erdocombining double acute accents, M. Steel, L. Szekely, and T. Warnow. A few logs suffice to build (almost) all trees (ii). Theoretical Computer Science, 221:77-118, 1999.
6. M. R. Garey and D. S. Johnson. Computers and Intractability; A Guide to the Theory of NP-Completeness. W.H. Freeman and Company, 1979.
7. M.X. Goemans and D.P. Williamson. Improved approximation algorithms for maximum cut and satisfiability problems using semidefinite programming. Journal of the Association for Computing Machinery, 42(6):1115-1145, November 1995.
8. I. Gronau, S. Moran, and S. Snir. Fast and reliable reconstruction of phylogenetic trees with very short branches. In ACM-SIAM Symposium on Discrete Algorithms (SODA), pages 379-388, 2008.
9. T. Jiang, P. Kearney, and M. Li. Orchestrating quartets: approximation and data correction. In IEEE Symp. Foundation of Computer Science (FOCS), pages 416-425, Palo Alto, California, November 1998.
10. T. Jiang, P. E. Kearney, and M. Li. A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM J. Comput., 30(6):1942-1961, 2000.
11. K. St. John, T. Warnow, B. M. E. Moret, and L. Vawter. Performance study of phylogenetic methods: (unweighted) quartet methods and neighbor-joining. In Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithms, 2001.
12. C. Semple and M.A. Steel. Phylogenetics. Oxford University Press, 2003.
13. S. Snir and S. Rao. Using max cut to enhance rooted trees consistency. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 3(4):323-333, 2006. Preliminary version appeared in WABI 2005.
14. S. Snir, T. Warnow, and S. Rao. Short quartet puzzling: A new quartet-based phylogeny reconstruction algorithm. Journal of Computational Biology (JCB), 1(15):91-103, 2008.
15. M. Steel. The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification, 9(1):91-116, 1992.