Parsimony via consensus

Systematic Biology

Volumn 57, Issue 2, 2008, Pages 251-256

  Bruen, Trevor C ^a   Bryant, David ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF AUCKLAND   (New Zealand)

Author keywords

Compatibility; Homoplasy; Maximum parsimony; SPR distance

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; PHYLOGENY; SPECIES DIFFERENTIATION;

COMPUTER SIMULATION; GENETIC SPECIATION; MODELS, GENETIC; PHYLOGENY;

EID: 54549085607     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150802040597     Document Type: Article

References (29)

1. Allen, B., and M. Steel. 2001. Subtree transfer operations and their induced metrics on evolutionary trees. Ann. Comb. 5:1-13.
2. Baum, B. 1992. Combining trees as a way of combining datasets for phylogenetic inference, and the desirability of combining gene trees. Taxon 41:3-10.
3. Bruen, T. 2006. Discrete and statistical approaches to genetics. PhD thesis, McGill University School of Computer Science, Montreal, Canada.
4. Bruen, T., and D. Bryant. 2008. A subdivision approach to maximum parsimony. Ann. Comb. 12:45-51.
5. Bruen, T., H. Philippe, and D. Bryant. 2006. A simple and robust statistical test to detect the presence of recombination. Genetics 172:1-17.
6. Bryant, D. 1997. Building trees, hunting for trees and comparing trees. PhD thesis, Department Mathematics, University of Canterbury, UK.
7. Bryant, D. 2003. A classification of consensus methods for phylogenetics. Pages 163-184 in Bioconsensus (M. F. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds.), volume 61 of DIMACS. American Mathematical Society, Providence, Rhode Island.
8. Bryant, D. 2004. The splits in the neighborhood of a tree. Ann. Combinatorics 8:1-11.
9. Chen, D., O. Eulenstein, D. Fernandez-Baca, and M. Sanderson. 2006. Minimum-flip supertrees: Complexity and algorithms. IEEE/ACM Trans. Comput. Biol. Bioinformatics 3:165-173.
10. Cotton, J., and M.Wilkinson. 2007. Majority-rule supertrees. Syst. Biol. 56:445-452.
11. Farris, J. S., M. Källersj ö, A. G. Kluge, and C. Bult. 1995. Constructing a significance test for incongruence. Syst. Biol. 44:570-572.
12. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
13. Fitch,W. M. 1971. Towards defining the course of evolution: Minimum change for a specific tree topology. Syst. Zool. 20:406-416.
14. Goloboff, P. 2007. Calculating SPR distances between trees. Cladistics 23:1-7.
15. Gordon, A. D. 1986. Consensus supertrees: The synthesis of rooted trees containing overlapping sets of labeled leaves. J. Class. 3:335-348.
16. Hein, J. 1990. Reconstructing evolution of sequences subject to recombination using parsimony. Math. Biosci. 98:185-200. (Pubitemid 20171457)
17. Hickey, G., F. Dehne, A. Rau-Chaplin, and C. Blouin. 2006. The computational complexity of the unrooted subtree prune and regraft distance. Tech. Rep. CS-2006-06. Faculty of Computer Science, Dalhousie University.
18. Hill, T. 2007. Development of new methods for inferring and evaluating phylogenetic trees. PhD thesis, Uppsala Universitet, Uppsala, Sweden.
19. Hudson, R. R., and N. L. Kaplan. 1985. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147-164. (Pubitemid 16248827)
20. Lapointe, F.-J., and G. Cucumel. 1997. The average consensus procedure: Combination of weighted taxa containing identical or overlapping sets of taxa. Syst. Biol. 46:306-312. (Pubitemid 127092068)
21. Le Quesne,W. J. 1969. Amethod of selection of characters in numerical taxonomy. Syst. Zool. 18:201-205.
22. Penny, D., and M. Hendy. 1986. Estimating the reliability of evolutionary trees. Mol. Biol. Evol. 3:403-417. (Pubitemid 16010522)
23. Ragan, M. A. 1992. Phylogenetic inference based on matrix representations of trees. Mol. Phyl. Evol. 1:53-58.
24. Sneath, P., M. Sackin, and R. Ambler. 1975. Detecting evolutionary incompatibilities from protein sequences. Systematic Zoology 24:311- 332.
25. Song, Y. S. 2003. On the combinatorics of rooted binary phylogenetic trees. Ann. Comb. 7:365-379. (Pubitemid 38069655)
26. Swofford, D., G. Olsen, P. Waddell, and D. Hillis. 1996. Molecular sytematics, Pages 407-514 in Phylogenetic inference. Sinauer Associates, Sunderland, Massachusetts.
27. Swofford, D. L. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland, Massachusetts.
28. Thorley, J. L., and M. Wilkinson. 2003. A view of supertree methods. Pages 185-194 in Bioconsensus (M. F. Janowitz, F.-J. Lapointe, F. R. McMorris, B. Mirkin, and F. S. Roberts, eds.), volume 61 of DIMACS, Series in Discrete Mathematics and Theoretical Computer Science, The American Mathematical Society, New York.
29. Zwickl, D. 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. PhD thesis, University of Texas at Austin.