Phylogenetic networks: Modeling, reconstructibility, and accuracy

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 1, Issue 1, 2004, Pages 13-23

  Moret, Bernard M E ^a   Nakhleh, Luay ^b   Warnow, Tandy ^b   Linder, C Randal ^c   Tholse, Anna ^a   Padolina, Anneke ^c   Sun, Jerry ^b   Timme, Ruth ^c  

^a University of New Mexico   (United States)

^b University of Texas at Austin   (United States)

^c UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Bipartitions; Error metric; Phylogenetic networks; Reticulate evolution; Robinson Foulds; Tripartitions

Indexed keywords

BIPARTITIONS; ERROR METRIC; PHYLOGENETIC NETWORKS; RETICULATE EVOLUTION; ROBINSON-FOULDS; TRIPATITIONS;

COMPUTATIONAL COMPLEXITY; COMPUTER SIMULATION; DATA ACQUISITION; ERROR ANALYSIS; GRAPH THEORY; MATHEMATICAL MODELS; MATHEMATICAL OPERATORS; METRIC SYSTEM; SET THEORY;

SYSTEMS SCIENCE;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; GENETIC RECOMBINATION; GENETICS; HORIZONTAL GENE TRANSFER; METHODOLOGY; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE TRANSFER, HORIZONTAL; MODELS, GENETIC; PHYLOGENY; RECOMBINATION, GENETIC;

EID: 4644360028     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2004.10     Document Type: Article

References (28)

1. L. Addario-Berry, M.T. Hallett, and J. Lagergren, "Toward Identifying Lateral Gene Transfer Events," Proc. Eighth Pacific Symp. Biocamputing (PSB '03), pp. 279-290, 2003.
2. H.J. Bandelt and A.W.M. Dress, "Split Decomposition: A New and Useful Approach to Phylogenetic Analysis of Distance Data," Molecular Phylogenetics and Evolution, vol. 1, pp. 242-252, 1992.
3. H.J. Bandelt, V. Macaulay, and M.B. Richards, "Median Networks: Speedy Construction and Greedy Reduction, One Simulation, and Two Case Studies from Human mtDNA," Molecular Phylogenetics and Evolution, vol. 16, pp. 8-28, 2000.
4. D. Bryant and V. Moulton, "NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks," Proc. Second Int'l Workshop Algorithms in Bioinformatics (WABI '02), pp. 375-391, 2002.
5. R.C. Griffiths and P. Marjoram, "Ancestral Inference from Samples of DNA Sequences with Recombination," J. Computational Biology, vol. 3, pp. 479-502, 1996.
6. M.T. Hallett and J. Lagergren, "New Algorithms for the Duplication-Loss Model," Proc. Fourth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '00), pp. 138-146, 2000.
7. M.T. Hallett and J. Lagergren, "Efficient Algorithms for Lateral Gene Transfer Problems," Proc. Fifth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '01), pp. 149-156, 2001.
8. M.T. Hallett, J. Lagergren, and A. Tofigh, "Simultaneous Identification of Duplications and Lateral Transfers," Proc. Eighth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '04), pp. 347-356, 2004.
9. D.M. Hillis, J.J. Bull, M.E. White, M.R. Badgett, and I.J. Molineux, "Experimental Approaches to Phylogenetic Analysis," Systematic Biology, vol. 42, pp. 90-92, 1993.
10. D.M. Hillis and J.P. Huelsenbeck, "Signal, Noise, and Reliability in Molecular Phylogenetic Analyses," J. Heredity, vol. 83, pp. 189-195, 1992.
11. R.R. Hudson, "Properties of the Neutral Allele Model with Intergenic Recombination," Theoretical Population Biology, vol. 23, pp. 183-201, 1983.
12. D.H. Huson, "SplitsTree: A Program for Analyzing and Visualising Evolutionary Data," Bioinformatics, vol. 14, no. 1, pp. 68-73, 1998.
13. W.P. Maddison, "Gene Trees in Species Trees," Systematic Biology, vol. 46, no. 3, pp. 523-536, 1997.
14. V. Makarenkov, "T-REX: Reconstructing and Visualizing Phylogenetic Trees and Reticulation Networks," Bioinformatics, vol. 17, no. 7, pp. 664-668, 2001.
15. V. Makarenkov and P. Legendre, "From a Phylogenetic Tree to a Reticulated Network," J. Computational Biology, vol. 11, no. 1, pp. 195-212, 2004.
16. L. Nakhleh, J. Sun, T. Warnow, R. Under, B.M.E. Moret, and A. Tholse, "Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods," Proc. Eighth Pacific Symp. Biocamputing (PSB '03), pp. 315-326, 2003.
17. L. Nakhleh, T. Warnow, and C.R. Linder, "Reconstructing Reticulate Evolution in Species - Theory and Practice," Proc. Eighth Ann. Int'l Conf. Computational Molecular Biology (RECOMB '04), pp. 337-346, 2004.
18. A. Piccolboni and D. Gusfield, "On the Complexity of Fundamental Computational Problems in Pedigree Analysis," Technical Report CSE-99-8, UC Davis, Dept. of Computer Science, 1999.
19. D. Posada and K.A. Crandall, "The Effect of Recombination on the Accuracy of Phylogeny Estimation," J. Molecular Evolution, vol. 54, no. 3, pp. 396-102, 2002.
20. D. Posada, K.A. Crandall, and E.C. Holmes, "Recombination in Evolutionary Genomics," Ann. Rev. Genetics, vol. 36, pp. 75-97, 2002.
21. L.H. Rieseberg, "The Role of Hybridization in Evolution - Old Wine in New Skins," Am. J. Botany, vol. 82, no. 7, pp. 944-953, 1995.
22. L.H. Rieseberg, S.J.E. Baird, and K.A. Gardner, "Hybridization, Introgression, and Linkage Evolution," Plant Molecular Biology, vol. 42, no. 1, pp. 205-224, 2000.
23. L.H. Rieseberg and R.D. Noyes, "Genetic Map-Based Studies of Reticulate Evolution in Plants," Trends in Plant Science, vol. 3, no. 7, pp. 254-259, 1998.
24. D.R. Robinson and L.R. Foulds, "Comparison of Phylogenetic Trees," Math. Biosciences, vol. 53, pp. 131-147, 1981.
25. F.J. Rohlf, "Phylogenetic Models and Reticulations," J. Classification, vol. 17, no. 2, pp. 185-189, 2000.
26. K. Strimmer and V. Moulton, "Likelihood Analysis of Phylogenetic Networks Using Directed Graphical Models," Molecular Biology and Evolution, vol. 17, pp. 875-881, 2000.
27. 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.
28. D.L. Swofford, G.J. Olsen, P.J. Waddell, and D.M. Hillis, "Phylogenetic Inference," Molecular Systematics, D.M. Hillis, B.K. Mable and C. Moritz, eds., pp. 407-514, Sinauer Assoc., 1996.