Consistency of the QNet algorithm for generating planar split networks from weighted quartets

Discrete Applied Mathematics

Volumn 157, Issue 10, 2009, Pages 2325-2334

  Grunewald S ^a,b   Moulton, V ^c   Spillner, A ^c  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^c UNIVERSITY OF EAST ANGLIA   (United Kingdom)

Author keywords

Circular split system; Phylogenetic network; Phylogenetic tree; Quartet tree; Split network

Indexed keywords

CIRCULAR SPLIT SYSTEM; PHYLOGENETIC NETWORK; PHYLOGENETIC TREE; QUARTET TREE; SPLIT NETWORK;

FUNCTION EVALUATION;

EID: 67349127662     PISSN: 0166218X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dam.2008.06.038     Document Type: Article

References (22)

1. Ben-Dor A., Chor B., Graur D., Ophir R., and Pelleg D. Constructing phylogenies from quartets: Elucidation of eutherian superordinal relationships. Journal of Computational Biology 5 (1998) 377-390
2. V. Berry, Méthodes et algorithmes pour reconstruire les arbres de l'Évolution, Ph.D. Thesis, Université de Montpellier, 1997
3. Berry V., and Gascuel O. Inferring evolutionary trees with strong combinatorial evidence. Theoretical Computer Science 240 (2000) 271-298
4. Berry V., Jiang T., Kearney P., Li M., and Wareham T. Quartet cleaning: Improved algorithms and simulations. In Proc. of European Symposium on Algorithms, ESA. LNCS vol. 1643 (1999), Springer 313-324
5. Bryant D., and Moulton V. NeighborNet: An agglomerative method for the construction of phylogenetic networks. Molecular Biology and Evolution 21 (2004) 255-265
6. Dress A., and Erdo{double acute}s P. X-trees and weighted quartet systems. Annals of Combinatorics 7 (2003) 155-169
7. Dress A., and Huson D. Constructing split graphs. IEEE Transactions on Computational Biology and Bioinformatics 1 (2004) 109-115
8. Felsenstein J. Inferring Phylogenies (2003), Sinauer Associates
9. Garey M.R., and Johnson D.S. Computers and Intractability: A Guide to the Theory of NP-Completeness (1979), W. H. Freeman
10. Gascuel O. BioNJ: An improved version of the NJ algorithm based on a simple model of sequence data. Molecular Biology and Evolution 14 (1997) 685-695
11. Grünewald S., Forslund K., Dress A., and Moulton V. QNet: An agglomerative method for the construction of phylogenetic networks from weighted quartets. Molecular Biology and Evolution 24 (2007) 532-538
12. Huber K., and Moulton V. Phylogenetic networks. In: Gascuel O. (Ed). Mathematics of Evolution (2005), Oxford University Press 178-200
13. Huson D., and Bryant D. Application of phylogenetic networks in evolutionary studies. Molecular Biology and Evolution 23 (2006) 254-267
14. Lawson C.L., and Hanson R.J. Solving Least Squares Problems (1974), Prentice-Hall
15. Morrison D. Networks in phylogenetic analysis: New tools for population biology. International Journal for Parasitology 35 (2005) 567-582
16. In: Pachter L., and Sturmfels B. (Eds). Algebraic Statistics for Computational Biology (2005), Cambridge University Press
17. Posada D., and Crandall K. Intraspecific gene genealogies: Trees grafting into networks. Trends in Ecology and Evolution 16 (2001) 37-45
18. Saitou N., and Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4 (1987) 406-425
19. Semple C., and Steel M. Phylogenetics (2003), Oxford University Press
20. Steel M. The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification 9 (1992) 91-116
21. Strimmer K., and von Haeseler A. Quartet puzzling: A quartet maximum likelihood method for reconstructing tree topologies. Molecular Biology and Evolution 13 (1996) 964-969
22. Weyer-Menkhoff J., Devauchelle C., Grossmann A., and Grünewald S. Integer linear programming as a tool for constructing trees from quartet data. Computational Biology and Chemistry 29 (2005) 196-203