Tripartitions do not always discriminate phylogenetic networks

Mathematical Biosciences

Volumn 211, Issue 2, 2008, Pages 356-370

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

^a UNIVERSITAT DE LES ILLES BALEARS   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

Bipartitions; Error metric; Phylogenetic networks; Recombination; Tripartition metric; Tripartitions

Indexed keywords

TREES (MATHEMATICS);

BIPARTITIONS; ERROR METRIC; PHYLOGENETIC NETWORKS; TRIPARTITION METRIC; TRIPARTITIONS;

GENE TRANSFER;

EVOLUTION; GENE TRANSFER; HYBRIDIZATION; PHYLOGENETICS; RECOMBINATION; RECONSTRUCTION;

ARTICLE; CLUSTER ANALYSIS; METRIC SYSTEM; MOLECULAR EVOLUTION; PHYLOGENY;

EVOLUTION, MOLECULAR; MODELS, GENETIC; PHYLOGENY;

EID: 38349011199     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2007.11.003     Document Type: Article

References (24)

1. Bandelt H.J. Phylogenetic networks. Verh. Naturwiss. Ver. Hambg. 34 (1994) 51
2. Baroni M., Semple C., and Steel M. Hybrids in real time. Syst. Biol. 55 (2006) 46
3. M. Bourque, Arbres de Steiner et réseaux dont varie l'emplagement de certains sommets, Ph.D. Thesis, Univ. de Montréal, 1978.
4. In: Burkhardt F., and Smith S. (Eds). The Correspondence of Charles Darwin vol. 2 (1987), Cambridge University
5. G. Cardona, F. Rosselló, G. Valiente, Comparison of tree-child phylogenetic networks, IEEE Trans. Comput. Biol. Bioinformat. (2008), in press, doi:10.1109/TCBB.2007.70270.
6. DasGupta B., He X., Jiang T., Li M., Tromp J., Wang L., and Zhang L. Computing distances between evolutionary trees. In: Du D.Z., and Pardalos P. (Eds). Handbook of Combinatorial Optimization (1998), Kluwer Academic Publishers 35
7. Doolittle W.F. Phylogenetic classification and the universal tree. Science 284 (1999) 2124
8. Felsenstein J. Inferring Phylogenies (2004), Sinauer Associated Inc.
9. Gusfield D., Eddhu S., and Langley C. The fine structure of galls in phylogenetic networks. Informs J. Comput. 16 (2004) 459
10. Gusfield D., Eddhu S., and Langley C. Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinformatics Comput. Biol. 2 (2004) 173
11. Jin G., Nakhleh L., Snir S., and Tuller T. Maximum likelihood of phylogenetic networks. Bioinformatics 22 (2006) 2604
12. Jin G., Nakhleh L., Snir S., and Tuller T. Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23 (2007) 123
13. C.R. Linder, B.M.E. Moret, L. Nakhleh, A. Padolina, J. Sun, A. Tholse, R. Timme, T. Warnow, An error metric for phylogenetic networks, Technical Report TR03-26, University of New Mexico, 2003.
14. C.R. Linder, B.M.E. Moret, L. Nakhleh, T. Warnow, Network (reticulate) evolution: biology, models, and algorithms, in: Tutorial presented at The Ninth Pacific Symposium on Biocomputing, 2003. Available from: .
15. B.M.E. Moret, L. Nakhleh, T. Warnow, An error metric for phylogenetic networks, Technical Report TR02-09, University of New Mexico, 2002.
16. Moret B.M.E., Nakhleh L., Warnow T., Linder C.R., Tholse A., Padolina A., Sun J., and Timme R. Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE Trans. Comput. Biol. 1 (2004) 13
17. L. Nakhleh, Phylogenetic networks, Ph.D. Thesis, University of Texas at Austin, 2004. Available from: .
18. L. Nakhleh, A. Clement, T. Warnow, C.R. Linder, B.M.E. Moret, Quality measures for phylogenetic networks, Technical Report TR04-06, University of New Mexico, 2004.
19. L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret, A. Tholse, Towards the development of computational tools for evaluating phylogenetic network reconstruction methods, in: Proceedings of 8th Pacific Symposium on Biocomputing, 2003, p. 315.
20. Robinson D.F., and Foulds L.R. Comparison of phylogenetic trees. Math. Biosci. 53 (1981) 131
21. Semple C., and Steel M. Phylogenetics. Oxford Lecture Series in Mathematics and Its Applications vol. 24 (2003), Oxford University
22. Strimmer K., and Moulton V. Likelihood analysis of phylogenetic networks using directed graphical models. Mol. Biol. Evol. 17 (2000) 875
23. Strimmer K., Wiuf C., and Moulton V. Recombination analysis using directed graphical models. Mol. Biol. Evol. 18 (2001) 97
24. S.J. Willson, Restrictions on meaningful phylogenetic networks, 2007. Available from: .