On the compatibility of quartet trees

Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Volumn , Issue , 2014, Pages 535-545

  Alon, Noga ^a,b   Snir, Sagi ^c   Yuster, Raphael ^c  

^a TEL AVIV UNIVERSITY   (Israel)

^b INSTITUTE FOR ADVANCED STUDY   (United States)

^c UNIVERSITY OF HAIFA   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS;

BIOLOGICAL PROBLEMS; CARDINALITIES; PHYLOGENETIC CLASSIFICATIONS; PHYLOGENETIC TREE RECONSTRUCTION; PHYLOGENETIC TREES; PROBABILISTIC ARGUMENTS; QUARTET DISTANCE; UPPER AND LOWER BOUNDS;

TREES (MATHEMATICS);

EID: 84902096374     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1137/1.9781611973402.40     Document Type: Conference Paper

References (33)

1. N. Alon and J.H. Spencer. The Probabilistic Method, 2nd edition. Wiley-Interscience, 2000.
2. H. Bandelt and A. Dress. Reconstructing the shape of a tree from observed dissimilarity data. Advances in Applied Mathematics, 7:309-343, 1986.
3. V. Berry and O. Gascuel. Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science, 240:271-298, 2001.
4. V. Berry, T. Jiang, P. Kearney, M. Li, and T. Warehain. Quartet cleaning: Improved algorithms and simulations. In European Symposium on Algorithms, 1999.
5. O. Bininda-Emonds. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Computational Biology. Springer, 2004.
6. O. Bininda-Emonds, J. Gittleman, and M. Steel. The (super)tree of life: Procedures, problems, and prospects. Annual Review of Ecology and Systematics, 33(1):265-289, 2002.
7. S. Bocker, D. Bryant, A. Dress, and M. Steel. Algorithmic aspects of tree amalgamation. Journal of Algorithms, 37(2):522-537, 2000.
8. D. Bryant and J. Lagergren. Compatibility of unrooted phylogenetic trees is FPT. Theoretical Computer Science, 351(3):296-302, 2006.
9. D. Bryant and M. Steel. Extension operations on sets of leaf-labelled trees. Advances in Applied Mathematics, 16(4):425-453, 1995.
10. D. Bryant and M. Steel. Constructing optimal trees from quartets. Journal of Algorithms, 38(1):237-259, 2001.
11. H. Colonius and H. Schulze. Tree structures for proximity data. British Journal of Mathematical and Statistical Psychology, 34(2):167-180, 1981.
12. M. Csürüs. Fast recovery of evolutionary trees with thousands of nodes. Journal of Computational Biology, 9(2):277-297, 2002.
13. Daskalakis E. Mossel, and S. Roch. Phylogenies without branch bounds: Contracting the short, pruning the deep. SIAM Journal on Discrete Mathematics, 25(2):872-893, 2011.
14. D. de Caen. Extension of a theorem of moon and moser on complete subgraphs. Ars Combinatoria, 16:5-10, 1983.
15. M. Dekker. Reconstruction methods for derivation trees, 1986. Masters thesis.
16. T. Dezulian and M. Steel. Phylogenetic closure operations and hoinoplasy-free evolution. In Classification, Clustering, and Data Mining Applications, Studies in Classification, Data Analysis, and Knowledge Organization, pages 395-416. Springer Berlin Heidelberg, 2004.
17. P. Erdos, 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.
18. P. Erdos, M. Steel, L. Szekely, and T. Warnow. A few logs suffice to build (almost) all trees (ii). Theoretical Computer Science, 221:77-118, 1999.
19. G. Estabrook, F. McMorris, and C. Meacham. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Systematic Biology, 34(2):193-200, 1985.
20. J. Estabrook. Comparison of undirected phylogenetic trees based on subtrees of four evolutionary units. Systematic Biology, 34(2):193-200, 1985.
21. I. Gronau, S. Moran, and S. Snir. Fast and reliable reconstruction of phylogenetic trees with indistinguishable edges. Random Structures and Algorithms, 40(3):350-384, 2012.
22. S. Griinewald. Slim sets of binary trees. Journal of Combinatorial Theory, Series A, 119(2):323-330, 2012.
23. S. Griinewald, M. Steel, and M. Shel Swenson. Closure operations in phylogenetics. Mathematical Biosciences, 208(2):521-537, 2007.
24. 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.
25. T. Jiang, P. Kearney, and M. Li. A polynomial time approximation scheme for inferring evolutionary trees from quartet topologies and its application. SIAM Journal on Computing, 30(6):1942-1961, 2000.
26. D.R. Robinson and L.R Foulds. Comparison of phylogenetic trees. Mathematical Biosciences, 53:131-147, 1981.
27. C. Semple and M.A. Steel. Phylogenetics. Oxford University Press, 2003.
28. S. Snir and S. Rao. Quartets maxcut: A divide and conquer quartets algorithm. Transactions on Computational Biology and Bioinformatics (TCBB), 7(4):714-718, 2010.
29. S. Snir and R. Yuster. A linear time approximation scheme for maximum quartet consistency on sparse sampled inputs. SIAM Journal on Discrete Mathematics, 25(4):1722-1736, 2011.
30. S. Snir and R. Yuster. Reconstructing approximate phylogenetic trees from quartet samples. SIAM Journal on Computing, 41(6): 1466-1480, 2012.
31. K. St. John, T. Warnow, B. 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.
32. M. Steel. The complexity of reconstructing trees from qualitative characters and subtress. Journal of Classification, 9(1):91-116, 1992.
33. K. Strimmer and A. von Haeseler. Quartet puzzling: A quartet maximum-likelihood method for reconstructing tree topologies. Molecular Biology and Evolution, 13(7):964-969, 1996. Software available at ftp://ftp.ebi.ac.uk/ pub/software/unix/puzzle/.