Fast computation of supertrees for compatible phylogenies with nested taxa

Systematic Biology

Volumn 55, Issue 2, 2006, Pages 270-288

  Berry, Vincent ^a   Semple, Charles ^b  

^a LIRMM   (France)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Compatibility; Nested taxa; Phylogenetics, strepsirrhine phylogeny; Supertree methods

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; COMPUTER PROGRAM; COMPUTER SIMULATION; GENETICS; PHYLOGENY; PROSIMIAN; TIME;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; PHYLOGENY; SOFTWARE; STREPSIRHINI; TIME FACTORS;

EID: 33744973813     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150500541649     Document Type: Review

References (24)

1. Aho, A. V., Y. Sagiv, T. G. Szymanski, and J. D. Ullman. 1981. Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10:405-421.
2. Berry, V. and O. Gascuel. 1996. On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain. Mol. Biol. Evol. 13:999-1011. (Pubitemid 26284916)
3. Bininda-Emonds, O. R. P., ed. 2004. Phylogenetic supertrees: Combining information to reveal the Tree of Life. Kluwer, Dordrecht.
4. Bininda-Emonds, O. R. P., K. E. Jones, S. A. Price, M. Cardillo, R. Grenyer, and A. Purvis. 2004. Garbage in, garbage out. Pages 267-280 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. R. P. Bininda-Emonds, ed.). Kluwer, Dordrecht.
5. Bordewich, M., G. Evans, and C. Semple. 2005. Extending the limits of supertree methods. Ann. of Comb, (in press).
6. Bryant, D. 1997. Building trees, hunting for trees, and comparing trees: Theory and methods in phylogenetic analysis. Ph.D. thesis, University of Canterbury.
7. Daniel, P., and C. Semple. 2004. Supertree algorithms for nested taxa. Pages 151-171 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. R. P. Bininda-Emonds, ed.). Kluwer, Dordrecht.
8. Daniel, P., and C. Semple. 2005. A class of general supertree methods for nested taxa. SIAM J. Discrete Math. 19:463-480. (Pubitemid 43774483)
9. Even, S., and Y. Shiloach. 1981. An on-line edge deletion problem. J. Assoc. Comput. Machinery 28:1-4.
10. Grünewald, S., M. Steel, and M. Swenson. 2005. Closure operations in phylogenetics. Tech. rep., University of Canterbury.
11. Henzinger, M. R., V. King, and T. Warnow. 1999. Constructing a tree from homeomorphic subtrees, with applications to computational evolutionary biology. Algorithmica 24:1-13.
12. Hibbett, D., R. H. Nilsson, M. Snyder, M. F. J. Costanzo, and M. Shonfeld. 2005. Automated phylogenetic taxonomy: An example in the homobasidiomycetes (mushroom-forming fungi). Syst.Biol. 54:660-668. (Pubitemid 41356475)
13. Holm, J., K. de Lichtenberg, and M. Thorup. 1998. Poly-logarithmic deterministic fully dynamic algorithms for connectivity, minimum spanning tree, 2-edge, and biconnectivity. Pages 78-89 in Proceedings of the 30th Annual ACM Symposium on Theory of Computing. ACM Press, New York.
14. Llabrés, M., J. Rocha, F. Rosselló, and G. Valiente. 2005. On the ancestral compatibility of two phylogenetic trees with nested taxa. Submitted.
15. Masters, J. C., and D. J. Brothers. 2002. Lack of congruence between morphological and molecular data in reconstructing the phylogeny of the galagonoidae. Am. J. Phys. Anthropol. 117:79-93. (Pubitemid 34024262)
16. Page, R. D. M. 2002. Modified mincut supertrees. Pages 537-552 in Second International Workshop on Algorithms in Bioinformatics (R. Guig and D. Gusfield, eds.). Springer, New York.
17. Page, R. D. M. 2004. Taxonomy, supertrees, and the tree of life. Pages 247-265 in Phylogenetic supertrees: Combining information to reveal the Tree of Life (O. R. P. Bininda-Emonds, ed.). Kluwer, Dordrecht.
18. Page, R. D. M., and G. Valiente. 2005. An edit script for taxonomy classifications. BMC Bioinformatics 6.
19. Roos, C., J. Schmitz, and H. Zischler. 2004. Primate jumping genes elucidates strepsirrhine phylogeny. Proc. Nat. Acad. Sci. 29:10650-10654. (Pubitemid 38955797)
20. Sanderson, M. J., B. G. Baldwin, G. Bharathan, C. S. Campbell, D. Ferguson, J. M. Porter, C. V. Dohlen, M. F. Wojciechowski, and M. J. Donoghue. 1993. The growth of phylogenetic information and the need for a phylogenetic database. Syst. Biol. 42:562-568. (Pubitemid 2031333)
21. Semple, C., and M. Steel. 2000. A supertree method for rooted trees. Discrete Appl. Math. 105:147-158.
22. Semple, C., and M. Steel. 2003. Phylogenetics. Oxford University Press, Oxford.
23. Yoder, A. D., R. M. Rasoloarison, S. M. Goodman, J. A. Irwin, S. Atsalis, M. J. Ravosa, and J. U. Ganzhorn. 2000. Remarkable species diversity in malagasy mouse lemurs (primates, microcebus). Proc. Nat. Acad. Sci. 97:11325-11330.
24. Zaroliagis, C. D. 2002. Implementations and experimental studies of dynamic graph algorithms. Pages 229-278 in Experimental algorithms: From algorithm design to robust and efficient software. Vol. 2547 of Lecture Notes in Computer Science, New York, Springer.