When two trees go to war

Journal of Theoretical Biology

Volumn 269, Issue 1, 2011, Pages 245-255

  van Iersel, Leo ^b   Kelk, Steven ^a  

^a CWI   (Netherlands)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Character; Cluster; Phylogenetic network; Reticulation; Triplet

Indexed keywords

NETWORK ANALYSIS; NUMERICAL MODEL; PARSIMONY ANALYSIS; PHYLOGENETICS;

ARTICLE; CLUSTER ANALYSIS; MATHEMATICAL MODEL; MOLECULAR PHYLOGENY; PARSIMONY ANALYSIS; PHYLOGENETIC TREE; PRIORITY JOURNAL;

CLUSTER ANALYSIS; MODELS, GENETIC; PHYLOGENY; RECOMBINATION, GENETIC;

EID: 78249242748     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.10.032     Document Type: Article

References (42)

1. Baroni M., Grünewald S., Moulton V., Semple C. Bounding the number of hybridisation events for a consistent evolutionary history. J. Math. Biol. 2005, 51:171-182.
2. Baroni M., Semple C., Steel M. Hybrids in real time. Syst. Biol. 2006, 55:46-56.
3. Bordewich M., Semple C. Computing the hybridization number of two phylogenetic trees is fixed-parameter tractable. IEEE/ACM Trans. Comput. Biol. Bioinform. 2007, 4(3):458-466.
4. Bordewich M., Semple C. Computing the minimum number of hybridization events for a consistent evolutionary history. Discrete Appl. Math. 2007, 155(8):914-928.
5. Bordewich M., Linz S., John K.S., Semple C. A reduction algorithm for computing the hybridization number of two trees. Evol. Bioinform. 2007, 3:86-98.
6. Bordewich M., Semple C., Spillner A. Optimizing phylogenetic diversity across two trees. Appl. Math. Lett. 2009, 22(5):638-641.
7. Collins, J., Linz, S., Semple, C., to appear. Quantifying hybridization in realistic time, J. Comput. Biol.
8. Gusfield, D., 2007. Different models for phylogenetic networks: How do they relate? Presentation at the Phylogenetics programme at the Isaac Newton Institute, Cambridge, UK.
9. Gusfield D., Eddhu S., Langley C. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol. 2004, 2:173-213.
10. Gusfield D., Bansal V., Bafna V., Song Y. A decomposition theory for phylogenetic networks and incompatible characters. J. Comput. Biol. 2007, 14(10):1247-1272.
11. Gusfield D., Hickerson D., Eddhu S. An efficiently computed lower bound on the number of recombinations in phylogenetic networks: theory and empirical study. Discrete Appl. Math. 2007, 155(6-7):806-830.
12. Huson, D.H., Klöpper, T.H., 2007. Beyond galled trees-decomposition and computation of galled networks. In: Research in Computational Molecular Biology (RECOMB), Lecture Notes in Computer Science, vol. 4453, pp. 211-225.
13. Huson, D.H., Rupp, R., 2008. Summarizing multiple gene trees using cluster networks. In: Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science, vol. 5251, pp. 296-305.
14. Huson D.H., Richter D.C., Rausch C., Franz M., Rupp R. Dendroscope: an interactive viewer for large phylogenetic trees. BMC Bioinform. 2007, 8(1):460.
15. Huson D.H., Rupp R., Berry V., Gambette P., Paul C. Computing galled networks from real data. Bioinformatics 2009, 25(12):i85-i93.
16. Huson, D.H., Rupp, R., Scornavacca, C., to appear. Phylogenetic Networks. Cambridge University Press.
17. Huynh, T.N.D., Jansson, J., Nguyen, N., Sung, W.-K., 2005. Constructing a smallest refining galled phylogenetic network. In: Research in Computational Molecular Biology (RECOMB), Lecture Notes in Bioinformatics, vol. 3500, pp. 265-280.
18. Jansson J., Sung W.-K. Inferring a level-1 phylogenetic network from a dense set of rooted triplets. Theor. Comput. Sci. 2006, 363(1):60-68.
19. Jansson J., Nguyen N.B., Sung W.-K. Algorithms for combining rooted triplets into a galled phylogenetic network. SIAM J. Comput. 2006, 35(5):1098-1121.
20. Kanj I.A., Nakhleh L., Than C., Xia G. Seeing the trees and their branches in the network is hard. Theor. Comput. Sci. 2008, 401(1-3):153-164.
21. Linz S., Semple C. Hybridization in non-binary trees. IEEE/ACM Trans. Comput. Biol. Bioinform. 2009, 6(1):30-45.
22. Lyngsø, R.B., Song, Y.S., Hein, J., 2005. Minimum recombination histories by branch and bound. In: Workshop on Algorithms in Bioinformatics (WABI), Lecture Notes in Computer Science, vol. 3692, pp. 239-250.
23. Myers S.R., Griffiths R.C. Bounds on the minimum number of recombination events in a sample history. Genetics 2003, 163:375-394.
24. Nakhleh L. Evolutionary phylogenetic networks: models and issues. The Problem Solving Handbook for Computational Biology and Bioinformatics 2009, Springer.
25. Phillips C., Warnow T.J. The asymmetric median tree-a new model for building consensus trees. Discrete Appl. Math. 1996, 71(1-3):311-335.
26. Semple C. Hybridization networks. Reconstructing Evolution-New Mathematical and Computational Advances 2007, 277-314. Oxford University Press.
27. Song Y., Wu Y., Gusfield D. Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution. Bioinformatics 2005, 21(Suppl. 1):i413-i422.
28. Song Y.S., Ding Z., Gusfield D., Langley C.H., Wu Y. Algorithms to distinguish the role of gene-conversion from single-crossover recombination in the derivation of SNP sequences in populations. J. Comput. Biol. 2007, 14(10):1273-1286.
29. To, T.-H., Habib, M., 2009. Level-k phylogenetic networks are constructable from a dense triplet set in polynomial time. In: Combinatorial Pattern Matching (CPM), Lecture Notes in Computer Science, vol. 5577, pp. 275-288.
30. van Iersel, L.J.J., Kelk, S.M., 2008a. Marlon: Constructing level one phylogenetic networks with a minimum amount of reticulation, http://homepages.cwi.nl/~kelk/marlon.html.
31. van Iersel, L.J.J., Kelk, S.M., 2008b. Simplistic: simple network heuristic, http://homepages.cwi.nl/~kelk/simplistic.html.
32. van Iersel, L.J.J., Kelk, S.M., to appear. Constructing the simplest possible phylogenetic network from triplets. Algorithmica.
33. van Iersel, L.J.J., Kelk, S.M., 2010. A short experiment to demonstrate a progressively larger tree-cluster gap, http://homepages.cwi.nl/~kelk/clusters/treeclus3treegap/.
34. van Iersel, L.J.J., Keijsper, J.C.M., Kelk, S.M., Stougie, L., 2007. Level2: a fast method for constructing level-2 phylogenetic networks from dense sets of rooted triplets, http://homepages.cwi.nl/~kelk/level2triplets.html.
35. van Iersel, L.J.J., Keijsper, J.C.M., Kelk, S.M., Stougie, L., Hagen, F., Boekhout, T., 2008. Constructing level-2 phylogenetic networks from triplets. In: Research in Computational Molecular Biology (RECOMB), Lecture Notes in Bioinformatics, vol. 4955, pp. 464-476.
36. van Iersel, L.J.J., Kelk, S.M., Rupp, R., Huson, D.H., 2009a. Cass: combining phylogenetic trees into a phylogenetic network, http://www.win.tue.nl/~liersel/cass.html.
37. van Iersel L.J.J., Keijsper J.C.M., Kelk S.M., Stougie L., Hagen F., Boekhout T. Constructing level-2 phylogenetic networks from triplets. IEEE/ACM Trans. Comput. Biol. Bioinform. 2009, 6(4):667-681.
38. van Iersel L.J.J., Kelk S.M., Rupp R., Huson D.H. Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters. Bioinformatics 2010, 26:i124-i131. (special issue: Proceedings of Intelligent Systems for Molecular Biology 2010 (ISMB2010), 10th-13th September 2010, Boston, USA.
39. Wang L., Zhang K., Zhang L. Perfect phylogenetic networks with recombination. J. Comput. Biol. 2001, 8(1):69-78.
40. Wu Y. Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees. Bioinformatics 2010, 26:i140-i148. (special issue: Proceedings of Intelligent Systems for Molecular Biology 2010 (ISMB2010), 10th-13th September 2010, Boston USA).
41. Wu, Y., Jiayin, W., 2010. Fast computation of the exact hybridization number of two phylogenetic trees, in: Bioinformatics Research and Applications (ISBRA), vol. 6053, pp. 203-214.
42. Wu Y., Gusfield D. A new recombination lower bound and the minimum perfect phylogenetic forest problem. J. Combin. Optim. 2008, 16(3):229-247.