Comparison of tree-child phylogenetic networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 6, Issue 4, 2009, Pages 552-569

  Cardona, Gabriel ^a   Rosselló, Francesc ^a   Valiente, Gabriel ^b  

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

Network alignment; Partition distance; Phylogenetic network; Phylogenetic tree; Tree child phylogenetic network

Indexed keywords

ALIGNMENT METHODS; BIPARTITION; DISTANCE MEASURE; EVOLUTIONARY EVENTS; JAVA APPLET; MULTI-SETS; NATURAL NUMBER; PATH MULTIPLICITY; PHYLOGENETIC NETWORKS; PHYLOGENETIC TREE; PHYLOGENETIC TREES; POLYNOMIAL ALGORITHM; PRACTICAL ALGORITHMS; REGULAR NETWORKS; ROBINSON-FOULDS DISTANCE;

GENE TRANSFER;

ALIGNMENT;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER; COMPUTER LANGUAGE; COMPUTER PROGRAM; HUMAN; INTERNET; METHODOLOGY; PHYLOGENY; SEQUENCE ALIGNMENT; STATISTICAL ANALYSIS; STATISTICAL MODEL; THEORETICAL MODEL;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTERS; DATA INTERPRETATION, STATISTICAL; HUMANS; INTERNET; MODELS, GENETIC; MODELS, STATISTICAL; MODELS, THEORETICAL; PHYLOGENY; PROGRAMMING LANGUAGES; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 75449092462     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2007.70270     Document Type: Article

References (48)

1. B.L. Allen and M.A. Steel, "Subtree Transfer Operations and Their Induced Metrics on Evolutionary Trees," Annals of Combinatorics, vol.5, no.1, pp. 1-13, 2001.
2. V. Bafna and V. Bansal, "The Number of Recombination Events in a Sample History: Conflict Graph and Lower Bounds," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol.1, no.2, pp. 78-90, Apr.-June 2004.
3. H.-J. Bandelt, "Phylogenetic Networks," Verhandl. Naturwiss. Vereins Hamburg, vol.34, pp. 51-71, 1994.
4. M. Baroni, C. Semple, and M. Steel, "A Framework for Representing Reticulate Evolution," Annals of Combinatorics, vol.8, no.4, pp. 391-408, 2004.
5. M. Baroni, C. Semple, and M. Steel, "Hybrids in Real Time," Systematic Biology, vol.55, no.1, pp. 46-56, 2006.
6. J. Bluis and D.-G. Shin, "Nodal Distance Algorithm: Calculating a Phylogenetic Tree Comparison Metric," Proc. Third IEEE Symp. BioInformatics and BioEng. (BIBE '03), pp. 87-94, 2003.
7. 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.
8. G. Cardona, F. Rosselló , and G. Valiente, "A Perl Package and an Alignment Tool for Phylogenetic Networks," BMC Boinformatics, vol.9, p. 175, 2008.
9. G. Cardona, F. Rosselló , and G. Valiente, "Tripartitions Do Not Always Discriminate Phylogenetic Networks," Math. Biosciences, vol.211, no.2, pp. 356-370, 2008.
10. D.E. Critchlow, D.K. Pearl, and C. Qian, "The Triples Distance for Rooted Bifurcating Phylogenetic Trees," Systematic Biology, vol.45, no.3, pp. 323-334, 1996.
11. B. DasGupta, X. He, T. Jiang, M. Li, J. Tromp, L. Wang, and L. Zhang, "Computing Distances between Evolutionary Trees," Handbook of Combinatorial Optimization, D.-Z. Du and P. Pardalos, eds., pp. 35-76, Kluwer Academic Publishers, 1998.
12. D. Gusfield, S. Eddhu, and C. Langley, "The Fine Structure of Galls in Phylogenetic Networks," INFORMS J. Computing, vol.16, no.4, pp. 459-469, 2004.
13. D. Gusfield, S. Eddhu, and C. Langley, "Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination," J. Bioinformatics and Computational Biology, vol.2, no.1, pp. 173-213, 2004.
14. D.H. Huson, "Tutorial: Introduction to Phylogenetic Networks," Proc. German Conf. Bioinformatics (GCB), tutorial, 2006.
15. D.H. Huson, "Split Networks and Reticulate Networks," Reconstructing Evolution: New Math. and Computational Advances, O. Gascuel and M. Steel, eds., pp. 247-276, Oxford Univ. Press, 2007.
16. D.H. Huson and D. Bryant, "Application of Phylogenetic Networks in Evolutionary Studies," Molecular Biology and Evolution, vol.23, no.2, pp. 254-267, 2006.
17. G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Maximum Likelihood of Phylogenetic Networks," Bioinformatics, vol.22, no.21, pp. 2604-2611, 2006.
18. G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Efficient Parsimony-Based Methods for Phylogenetic Network Reconstruction," Bioinformatics, vol.23, no.2, pp. 123-128, 2007.
19. H.W. Kuhn, "The Hungarian Method for the Assignment Problem," Naval Research Logistics Quarterly, vol.2, pp. 83-97, 1955.
20. C.R. Linder, B.M.E. Moret, L. Nakhleh, A. Padolina, J. Sun, A. Tholse, R. Timme, and T. Warnow, "An Error Metric for Phylogenetic Networks," Technical Report TR03-26, Univ. of New Mexico, 2003.
21. C.R. Linder, B.M.E. Moret, L. Nakhleh, and T. Warnow, "Network (Reticulate) Evolution: Biology, Models, and Algorithms," Proc. Ninth Pacific Symp. Biocomputing (PSB), tutorial, 2003.
22. W.P. Maddison, "Gene Trees in Species Trees," Systematic Biology, vol.46, no.3, pp. 523-536, 1997.
23. B.M.E. Moret, "Computational Challenges from the Tree of Life," Proc. Seventh Workshop Algorithm Eng. and Experiments and Second Workshop Analytic Algorithmics and Combinatorics, pp. 3-16, 2005.
24. B.M.E. Moret, L. Nakhleh, and T. Warnow, "An Error Metric for Phylogenetic Networks," Technical Report TR02-09, Univ. of New Mexico, 2002.
25. B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, "Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol.1, no.1, pp. 13-23, Jan.-Mar. 2004.
26. J. Munkres, "Algorithms for the Assignment and Transportation Problems," J. SIAM, vol.5, no.1, pp. 32-38, 1957.
27. T. Munzner, F. Guimbretière, S. Tasiran, L. Zhang, and Y. Zhou, "TreeJuxtaposer: Scalable Tree Comparison Using Focus+Context with Guaranteed Visibility," ACM Trans. Graphics, vol.22, no.3, pp. 453-462, 2003.
28. S.R. Myers and R.C. Griffiths, "Bounds on the Minimum Number of Recombination Events in a Sample History," Genetics, vol.163, no.1, pp. 375-394, 2003.
29. L. Nakhleh, "Phylogenetic Networks," PhD dissertation, Univ. of Texas, Austin, 2004.
30. L. Nakhleh, A. Clement, T. Warnow, C.R. Linder, and B.M.E. Moret, "Quality Measures for Phylogenetic Networks," Technical Report TR04-06, Univ. of New Mexico, 2004.
31. L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret, and A. Tholse, "Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods," Proc. Eighth Pacific Symp. Biocomputing (PSB '03), pp. 315-326, 2003.
32. L. Nakhleh, T. Warnow, C.R. Linder, and K.S. John, "Reconstructing Reticulate Evolution in Species: Theory and Practice," J. Computational Biology, vol.12, no.6, pp. 796-811, 2005.
33. T.M. Nye, P. Lio, and W.R. Gilks, "A Novel Algorithm and Web-Based Tool for Comparing Two Alternative Phylogenetic Trees," Bioinformatics, vol.22, no.1, pp. 117-119, 2006.
34. R.D.M. Page, "Parallel Phylogenies: Reconstructing the History of Host-Parasite Assemblages," Cladistics, vol.10, no.2, pp. 155-173, 1995.
35. R.D.M. Page, "Phyloinformatics: Toward a Phylogenetic Database," Data Mining in Bioinformatics, J.T.-L. Wang, M.J. Zaki, H. Toivonen, and D. Shasha, eds., pp. 219-241, Springer, 2005.
36. R.D.M. Page and G. Valiente, "An Edit Script for Taxonomic Classifications," BMC Bioinformatics, vol.6, p. 208, 2005.
37. P. Puigbò , S. Garcia-Vallvé, and J.O. McInerney, "TOPD/FMTS: A New Software to Compare Phylogenetic Trees," Bioinformatics, vol.23, no.12, pp. 1556-1558, 2007.
38. D.F. Robinson and L.R. Foulds, "Comparison of Phylogenetic Trees," Math. Biosciences, vol. 53, no. 1/2, pp. 131-147, 1981.
39. C. Semple, "Hybridization Networks," Reconstructing Evolution: New Mathematical and Computational Advances, O. Gascuel and M. Steel, eds., Oxford Univ. Press, 2007.
40. Y.S. Song, J. Hein, "Constructing Minimal Ancestral Recombination Graphs," J. Computational Biology, vol.12, no.2, pp. 147-169, 2005.
41. K. Strimmer and V. Moulton, "Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models," Molecular Biology and Evolution, vol.17, no.6, pp. 875-881, 2000.
42. K. Strimmer, C. Wiuf, and V. Moulton, "Recombination Analysis Using Directed Graphical Models," Molecular Biology and Evolution, vol.18, no.1, pp. 97-99, 2001.
43. L. Wang, K. Zhang, and L. Zhang, "Perfect Phylogenetic Networks with Recombination," J. Computational Biology, vol.8, no.1, pp. 69-78, 2001.
44. M.S. Waterman and T.F. Smith, "On the Similarity of Dendograms," J. Theoretical Biology, vol.73, no.4, pp. 789-800, 1978.
45. S.J. Willson, "Unique Solvability of Certain Hybrid Networks from Their Distances," Annals of Combinatorics, vol.10, no.1, pp. 165-178, 2006.
46. S.J. Willson, "Reconstruction of Some Hybrid Phylogenetic Networks with Homoplasies from Distances," Bull. of Math. Biology, vol.69, no.8, pp. 2561-2590, 2007.
47. S.J. Willson, "Restrictions on Meaningful Phylogenetic Networks," Proc. Workshop Current Challenges and Problems in Phylogenetics, accepted contributed talk, Sept. 2007.
48. S.J. Willson, "Unique Determination of Some Homoplasies at Hybridization Events," Bull. of Math. Biology, vol.69, no.5, pp. 1709-1725, 2007.