Reconstructing an ultrametric galled phylogenetic network from a distance matrix

Journal of Bioinformatics and Computational Biology

Volumn 4, Issue 4, 2006, Pages 807-832

  Chan, Ho Leung ^a   Jansson, Jesper ^b   Lam, Tak Wah ^a   Yiu, Siu Ming ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b KYUSHU UNIVERSITY   (Japan)

Author keywords

Algorithm; Distance based reconstruction; Phylogenetic network; Ultrametric galled network

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENETIC ALGORITHM; GENETIC DISTANCE; MATHEMATICAL ANALYSIS; MOLECULAR EVOLUTION; PHYLOGENETIC TREE CONSTRUCTION METHOD; PHYLOGENETIC TREE ROOT; PROBLEM SOLVING; SPECIES; STATISTICAL PARAMETERS;

ALGORITHMS; CHROMOSOME MAPPING; COMPUTER SIMULATION; EVOLUTION; EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY; QUANTITATIVE TRAIT LOCI; SEQUENCE ANALYSIS, DNA;

EID: 33750453742     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720006002211     Document Type: Article

References (28)

1. AT&T Bell Laboratories, Graphviz - graph visualization software, http://www.graphviz.org.
2. Auburn University, Drawing graphs with VGJ. http://www.eng.auburn.edu/ department/cse/research/graph_drawing/graph_drawing.html.
3. Bryant D, Building trees, hunting for trees, and comparing trees: Theory and methods in phylogenetic analysis, Ph.D. Thesis, University of Canterbury, Christchurch, New Zealand, 1997.
4. Bryant D, Moulton V, Neighbor-Net: An agglomerative method for the construction of phylogenetic networks, Mol Biol Evol 21:255-265, 2004.
5. Chen H-F, Chang M-S, An efficient exact algorithm for the minimum ultrametric tree problem, Proc. 15th Int Symp Algorithms Comput (ISAAC 2004), Vol. 3341 of LNCS, Springer, pp. 282-293, 2004.
6. Choy C et al., Computing the maximum agreement of phylogenetic networks, Theor Comput Sci 335:93-107, 2005.
7. Day WE, Computational complexity of inferring phylogenies from dissimilarity matrices, Bulletin Math Biol 49:461-467, 1987.
8. Diday E, Bertrand P, An extension of hierarchical clustering: The pyramidal representation, Pattern Recogn in Practice II, 411-424, 1986.
9. Farach M, Kannan S, Warnow T, A robust model for finding optimal evolutionary trees, Algorithmica 13:155-179, 1995.
10. Gansner E, Koutsofios E, North S, Drawing graphs with dot, http://www.research.att.com/sw/tools/graphviz/dotguide.pdf.
11. Garey M, Johnson D, Computers and Intractability - A Guide to the Theory of NP-Completeness, W. H. Freeman and Company, New York, 1979.
12. Gusfield D, Algorithms on Strings, Trees, and Sequences, Cambridge University Press, New York, 1997.
13. Gusfield D, Bansal V, A fundamental decomposition theory for phylogenetic networks and incompatible characters, Proc 9th Annual Int Conf Res Comput Mol Biol (RECOMB 2005), Vol. 3500 of LNCS, Springer-Verlag, Berlin, Heidelberg, pp. 217-232, 2005.
14. Gusfield D, Eddhu S, Langley C, Optimal, efficient reconstruction of phylogenetic networks with constrained recombination, J Bioinf Computat Biol 2:173-213, 2004.
15. He Y-J et al. Inferring phylogenetic relationships avoiding forbidden rooted triplets, J Bioinf Comput Biol 4:59-74, 2006.
16. Himsolt M, GML: A portable graph file format, http://infosun.fmi.uni-passau.de/Graphlet/GML/gml-tr.html.
17. Holland B, Moulton V, Consensus networks: A method for visualising incompatibilities in collections of trees, Proc 3rd Workshop Algorithms Bioinf (WABI 2003), Vol. 2812 of LNCS, Springer-Verlag, Berlin, Heidelberg, pp. 165-176, 2003.
18. Huson DH et al., Phylogenetic super-networks from partial trees, Proc 4th Workshop Algorithms Bioinfor (WABI 2004), Vol. 3240 of LNCS, Springer, pp. 388-399, 2004.
19. Huynh TND et al., Constructing a smallest refining galled phylogenetic network, Proc 9th Annual Int Conf Res Comput Mol Biol (RECOMB 2005), Vol. 3500 of LNCS, Springer-Verlag, Berlin, Heidelberg, pp. 265-280, 2005.
20. Jansson J, Nguyen NB, Sung W-K, Algorithms for combining rooted triplets into a galled phylogenetic network, SIAM J Comput 35:1098-1121, 2006.
21. Jansson J, Sung Y, The maximum agreement of two nested phylogenetic networks, Proc 15th Int Symp Algorithms Comput (ISAAC 2004), Vol. 3341 of LNCS, Springer-Verlag, Berlin, Heidelberg, pp. 581-593, 2004.
22. Linder CR et al., Network (reticulate) evolution: Biology, models, and algorithms, Tutorial presented at the 9th Pac Symp Biocomputing (PSB 2004), 2004.
23. Nakhleh L, Warnow T, Linder CR, Reconstructing reticulate evolution in species - theory and practice, Proc 8th Annual Int Conf Res Comput Mole Biol (RECOMB 2004), pp. 337-346, 2004.
24. Posada D, Crandall KA, Intraspecific gene genealogies: Trees grafting into networks, TRENDS Ecolo & Evol 16:37-45, 2001.
25. Saitou N, Nei M, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Mole Biol Evol 4:406-425, 1987.
26. Setubal JC, Meidanis J, Introduction to Computational Molecular Biology, PWS Publishing Company, Boston, 1997.
27. Wang L, Zhang K, Zhang L, Perfect phylogenetic networks with recombination, J Comput Biol 8:69-78, 2001.
28. Wu BY, Chao K-M, Tang CY, Approximation and exact algorithms for constructing minimum ultrametric trees from distance matrices, J Comb Optimization 3:199-211, 1999.