The Community for Technology Leaders
RSS Icon
Subscribe
Issue No.04 - July/August (2011 vol.8)
pp: 1141-1147
Sylvain Guillemot , Institut Gaspard Monge, Marne-la-Vallee
Jesper Jansson , Ochanomizu University, Tokyo
Wing-Kin Sung , National University of Singapore, Singapore
ABSTRACT
HASH(0x295bbbc)
INDEX TERMS
Phylogenetics; MUL tree; rooted triplet; acyclic tree-partition; inapproximability; dynamic programming.
CITATION
Sylvain Guillemot, Jesper Jansson, Wing-Kin Sung, "Computing a Smallest Multilabeled Phylogenetic Tree from Rooted Triplets", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 4, pp. 1141-1147, July/August 2011, doi:10.1109/TCBB.2010.77
REFERENCES
[1] A.V. Aho, J.E. Hopcroft, and J.D. Ullman, The Design and Analysis of Computer Algorithms. Addison-Wesley, 1974.
[2] A.V. Aho, Y. Sagiv, T.G. Szymanski, and J.D. Ullman, “Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions,” SIAM J. Computing, vol. 10, no. 3, pp. 405-421, 1981.
[3] V. Berry and F. Nicolas, “Maximum Agreement and Compatible Supertrees,” J. Discrete Algorithms, vol. 5, no. 3, pp. 564-591, 2007.
[4] G.K. Brown, G. Nelson, and P.Y. Ladiges, “Historical Biogeography of Rhododendron Section Vireya and the Malesian Archipelago,” J. Biogeography, vol. 33, no. 11, pp. 1929-1944, 2006.
[5] J. Byrka, S. Guillemot, and J. Jansson, “New Results on Optimizing Rooted Triplets Consistency,” Discrete Applied Math., vol. 158, no. 11, pp. 1136-1147, 2010.
[6] J. Chen, Y. Liu, S. Lu, B. O'Sullivan, and I. Razgon, “A Fixed-Parameter Algorithm for the Directed Feedback Vertex Set Problem,” J. ACM, vol. 55, no. 5,article no. 21, 2008.
[7] B. Chor, M. Hendy, and D. Penny, “Analytic Solutions for Three Taxon ML Trees with Variable Rates across Sites,” Discrete Applied Math., vol. 155, nos. 6-7, pp. 750-758, 2007.
[8] U. Feige and J. Kilian, “Zero Knowledge and the Chromatic Number,” J. Computer and System Sciences, vol. 57, no. 2, pp. 187-199, 1998.
[9] M. Fellows, M. Hallett, and U. Stege, “Analogs & Duals of the MAST Problem for Sequences & Trees,” J. Algorithms, vol. 49, no. 1, pp. 192-216, 2003.
[10] G. Ganapathy, B. Goodson, R. Jansen, H.-S. Le, V. Ramachandran, and T. Warnow, “Pattern Identification in Biogeography,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 334-346, Oct.-Dec. 2006.
[11] M. Garey and D. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W. H. Freeman, 1979.
[12] S. Guillemot and V. Berry, “Fixed-Parameter Tractability of the Maximum Agreement Supertree Problem,” Proc. 18th Ann. Symp. Combinatorial Pattern Matching (CPM '07), pp. 274-285, 2007.
[13] M.R. Henzinger, V. King, and T. Warnow, “Constructing a Tree from Homeomorphic Subtrees, with Applications to Computational Evolutionary Biology,” Algorithmica, vol. 24, no. 1, pp. 1-13, 1999.
[14] J. Holm, K. de Lichtenberg, and M. Thorup, “Poly-logarithmic Deterministic Fully-Dynamic Algorithms for Connectivity, Minimum Spanning Tree, 2-Edge, and Biconnectivity,” J. ACM, vol. 48, no. 4, pp. 723-760, 2001.
[15] K.T. Huber, M. Lott, V. Moulton, and A. Spillner, “The Complexity of Deriving Multi-Labeled Trees from Bipartitions,” J. Computational Biology, vol. 15, no. 6, pp. 639-651, 2008.
[16] K.T. Huber and V. Moulton, “Phylogenetic Networks from Multi-Labelled Trees,” J. Math. Biology, vol. 52, no. 5, pp. 613-632, 2006.
[17] K.T. Huber, B. Oxelman, M. Lott, and V. Moulton, “Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees,” Molecular Biology and Evolution, vol. 23, no. 9, pp. 1784-1791, 2006.
[18] J. Jansson, J.H.-K. Ng, K. Sadakane, and W.-K. Sung, “Rooted Maximum Agreement Supertrees,” Algorithmica, vol. 43, no. 4, pp. 293-307, 2005.
[19] V. Neumann-Lara, “The Dichromatic Number of a Digraph,” J. Combinatorial Theory, Series B, vol. 33, no. 3, pp. 265-270, 1982.
[20] R.D.M. Page and M.A. Charleston, “Trees within Trees: Phylogeny and Historical Associations,” Trends in Ecology & Evolution, vol. 13, no. 9, pp. 356-359, 1998.
[21] C. Scornavacca, V. Berry, and V. Ranwez, “From Gene Trees to Species Trees through a Supertree Approach,” Proc. Third Int'l Conf. Language and Automata Theory and Applications (LATA '09), pp. 702-714, 2009.
[22] P.D. Seymour, “Packing Directed Circuits Fractionally,” Combinatorica, vol. 15, no. 2, pp. 281-288, 1995.
[23] D. Zuckerman, “Linear Degree Extractors and the Inapproximability of Max Clique and Chromatic Number,” Theory of Computing, vol. 3, no. 1, pp. 103-128, 2007.
[24] J. Jansson, R.S. Lemence, and A. Lingas, “The Complexity of Inferring a Minimally Resolved Phylogenetic Supertree,” Proc. 10th Int'l Workshop Algorithms in Bioinformatics (WABI '10), pp. 262-273, 2010.
18 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool