On the elusiveness of clusters

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 2, 2012, Pages 517-534

  Kelk, Steven ^a   Scornavacca, Celine ^b   Van Iersel, Leo ^c  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b UNIVERSITY OF TÜBINGEN   (Germany)

^c UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

clusters; computational complexity; parsimony; polynomial time algorithms; reticulate evolution; Rooted phylogenetic networks

Indexed keywords

CLUSTERS; PARSIMONY; PHYLOGENETIC NETWORKS; POLYNOMIAL-TIME ALGORITHMS; RETICULATE EVOLUTION;

BINARY TREES; COMPUTATIONAL COMPLEXITY; FORESTRY; GENES; POLYNOMIALS; TREES (MATHEMATICS);

CLUSTERING ALGORITHMS;

ALGORITHMS; FORESTRY; GENES; MATHEMATICS; TREES;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; CLUSTER ANALYSIS; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY; PROCEDURES;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 84856431535     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.128     Document Type: Article

References (32)

1. C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
2. Mathematics of Evolution and Phylogeny, O. Gascuel, ed. Oxford Univ. Press, Inc., http://portal.acm.org/citation.cfm?id=1557209, 2005.
3. Reconstructing Evolution: New Mathematical and Computational Advances, O. Gascuel and M. Steel, eds. Oxford Univ. Press, http://www.amazon.com/exec/ obidos/redirect?tag=citeulike07-20&path=ASIN/0199208220, 2007.
4. D.H. Huson, R. Rupp, and C. Scornavacca, Phylogenetic Networks: Concepts, Algorithms and Applications. Cambridge Univ. Press, 2011.
5. L. Nakhleh,"Evolutionary Phylogenetic Networks: Models and Issues," The Problem Solving Handbook for Computational Biology and Bioinformatics, Springer, 2009.
6. C. Semple,"Hybridization Networks," Reconstructing Evolution -New Mathematical and Computational Advances, Oxford Univ. Press, 2007.
7. D.H. Huson, R. Rupp, V. Berry, P. Gambette, and C. Paul,"Computing Galled Networks from Real Data," Bioinformatics, vol. 25, no. 12, pp. i85-i93, 2009.
8. L.J.J. van Iersel and S.M. Kelk,"When Two Trees Go to War," J. Theoretical Biology, vol. 269, no. 1, pp. 245-255, 2011.
9. J. Jansson and W.-K. Sung,"Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets," Theoretical Computer Science, vol. 363, no. 1, pp. 60-68, 2006. (Pubitemid 44508784)
10. J. Jansson, N.B. Nguyen, and W.-K. Sung,"Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network," SIAM J. Computing, vol. 35, no. 5, pp. 1098-1121, 2006. (Pubitemid 44599920)
11. L.J.J. van Iersel, J.C.M. Keijsper, S.M. Kelk, L. Stougie, F. Hagen, and T. Boekhout,"Constructing Level-2 Phylogenetic Networks from Triplets," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 667-681, Oct.-Dec. 2009.
12. L.J.J. van Iersel, S.M. Kelk, and M. Mnich,"Uniqueness, Intractability and Exact Algorithms: Reflections on Level-k Phylogenetic Networks," J. Bioinformatics and Computational Biology, vol. 7, no. 2, pp. 597-623, 2009.
13. T.-H. To and M. Habib,"Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time," Proc. Conf. Combinatorial Pattern Matching (CPM '09), pp. 275-288, 2009.
14. M. Bordewich and C. Semple,"Computing the Minimum Number of Hybridization Events for a Consistent Evolutionary History," Discrete Applied Math., vol. 155, no. 8, pp. 914-928, 2007. (Pubitemid 46436152)
15. M. Bordewich, S. Linz, K.S. John, and C. Semple,"A Reduction Algorithm for Computing the Hybridization Number of Two Trees," Evolutionary Bioinformatics, vol. 3, pp. 86-98, 2007.
16. M. Bordewich and C. Semple,"Computing the Hybridization Number of Two Phylogenetic Trees Is Fixed-Parameter Tractable," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 4, no. 3, pp. 458-466, July-Sept. 2007. (Pubitemid 47274721)
17. J. Collins, S. Linz, and C. Semple,"Quantifying Hybridization in Realistic Time," J. Computational Biology, vol. 18, no. 10, pp 1305-1318, 2011.
18. Y. Wu and W. Jiayin,"Fast Computation of the Exact Hybridization Number of Two Phylogenetic Trees," Proc. Sixth Int'l Symp. Bioinformatics Research and Applications (ISBRA), vol. 6053, pp. 203-214, 2010.
19. Y. Wu,"Close Lower and Upper Bounds for the Minimum Reticulate Network of Multiple Phylogenetic Trees," Bioinformatics, vol. 26, pp. i140-i148, 2010.
20. T. Huynh, J. Jansson, N. Nguyen, and W.-K. Sung,"Constructing a Smallest Refining Galled Phylogenetic Network," Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 265-280, 2005. (Pubitemid 41420669)
21. L. van Iersel and S. Kelk,"Constructing the Simplest Possible Phylogenetic Network from Triplets," Algorithmica, pp. 1-29, Springer, http://dx.doi.org/10.1007/s00453-009-9333-0, 2009.
22. D. Gusfield, V. Bansal, V. Bafna, and Y. Song,"A Decomposition Theory for Phylogenetic Networks and Incompatible Characters," J. Computational Biology, vol. 14, no. 10, pp. 1247-1272, 2007. (Pubitemid 350249340)
23. D. Gusfield, D. Hickerson, and S. Eddhu,"An Efficiently Computed Lower Bound on the Number of Recombinations in Phylognetic Networks: Theory and Empirical Study," Discrete Applied Math., vol. 155, nos. 6/7, pp. 806-830, 2007. (Pubitemid 46215768)
24. Y. Wu and D. Gusfield,"A New Recombination Lower Bound and the Minimum Perfect Phylogenetic Forest Problem," J. Combinatorial Optimization, vol. 16, no. 3, pp. 229-247, 2008.
25. S.R. Myers and R.C. Griffiths,"Bounds on the Minimum Number of Recombination Events in a Sample History," Genetics, vol. 163, pp. 375-394, 2003. (Pubitemid 36222680)
26. D.H. Huson and T.H. Klöpper,"Beyond Galled Trees-Decomposition and Computation of Galled Networks," Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 211-225, 2007. (Pubitemid 47164542)
27. L.J.J. van Iersel, S.M. Kelk, R. Rupp, and D.H. Huson,"Phylogenetic Networks Do Not Need to be Complex: Using Fewer Reticulations to Represent Conflicting Clusters," Bioinformatics, vol. 26, pp. i124-i131, 2010.
28. D. Huson and C. Scornavacca,"Dendroscope 3-A Program for Computing and Drawing Rooted Phylogenetic Trees and Networks," in Preparation. Software Available from: www. dendroscope.org, 2011.
29. S. Linz and C. Semple,"Hybridization in Non-Binary Trees," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 30-45, Jan.-Mar. 2009.
30. P. Gambette, V. Berry, and C. Paul,"The Structure of Level-k Phylogenetic Networks," Proc. 20th Ann. Symp. Combinatorial Pattern Matching, pp. 289-300, http://dx.doi.org/10.1007/978-3-642-02441-2-26, 2009.
31. P. Gambette,"Generators -Building Level-k Generators," http:// www.lirmm.fr/gambette/ProgGenerators.php, 2011.
32. V. Bafna and V. Bansal,"Inference about Recombination from Haplotype Data: Lower Bounds and Recombination Hotspots," J. Computational Biology, vol. 13, pp. 501-521, 2006.