Groves of phylogenetic trees

Annals of Combinatorics

Volumn 13, Issue 2, 2009, Pages 139-167

  Ané, Cécile ^a   Eulenstein, Oliver ^b   Piaggio Talice, Raul ^b   Sanderson, Michael J ^c  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Iowa State University   (United States)

^c University of Arizona   (United States)

Author keywords

Clustering; Evolution; Supermatrix; Supertree; Triplets

Indexed keywords

EID: 70349895336     PISSN: 02180006     EISSN: 02193094     Source Type: Journal    
DOI: 10.1007/s00026-009-0017-x     Document Type: Article

References (20)

1. Aho A.V., Sagiv Y., Szymanski T.G., Ullman J.D.: Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10(3), 405-421 (1981).
2. Bininda-Emonds O.R.P.: Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, Computational Biology, Vol. 4. Kluwer Academic Publishers, Dordrecht (2004).
3. Bininda-Emonds O.R.P., Gittleman J.L., Steel M.: The (super)tree of life: procedures, problems, and prospects. Annu. Rev. Ecol. Syst. 33, 265-289 (2002).
4. Bryant D.J., Steel M.: Extension operations on sets of leaf-labelled trees. Adv. Appl. Math. 16(4), 425-453 (1995).
5. Cotton J.A., Slater C.S.C., Wilkinson M.: Discriminating supported and unsupported relationships in supertrees using triplets. Syst. Biol. 55(2), 345-350 (2006).
6. Davies T.J., Barraclough T.G., Chase M.W., Soltis P.S., Soltis D.E., Savolainen V.: Darwin's abominable mystery: insights from a supertree of the angiosperms. Proc. Natl. Acad. Sci. USA 101, 1904-1909 (2004).
7. Driskell A.C., Burleigh J.G., Burleigh J.G., McMahon M.M., O'Meara B.C., Sanderson M.J.: Prospects for building the tree of life from large sequence databases. Science 306, 1172-1174 (2004).
8. Foulds L.R., Graham R.L.: The Steiner problem in Phylogeny is NP-complete. Adv. Appl. Math. 3, 43-49 (1982).
9. Hall M. Jr.: Combinatorial Theory. John Wiley & Sons, New York (1986).
10. Kennedy M., Page R.D.M.: Seabird supertrees: combining partial estimates of procellariiform phylogeny. Auk 119(1), 88-108 (2002).
11. Liu F.-G., Miyamoto M.M., Freire N.P., Ong P.Q., Tennant M.R., Young T.S., Gugel K.F.: Molecular and morphological supertrees for eutherian (plancental) mammals. Science 291, 1786-1789 (2001).
12. R.D.M. Page, Phyloinformatics: towards a phylogenetic database, In: Data Mining in Bioinformatics, J.T.L.Wang, M.J. Zaki, H.T.T. Toivonen, and D.E. Shasha, Eds., Springer, Heidelberg, (2005) pp. 219-241.
13. R.D.M. Page, Taxonomy, supertrees, and the Tree of Life, In: Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life, O.R.P. Bininda-Emonds Ed., Kluwer Academic Publishers, Dordrecht, (2004) pp. 247-265.
14. Papadimitriou C.H.: Computational Complexity. Addison-Wesley, Reading, Massachusetts (1994).
15. Pisani D., Yates A.M., Langer M.C., Benton M.J.: A genus-level supertree of the Dinosauria. Proc. R. Soc. Lond. B 269, 915-921 (2002).
16. M.J. Sanderson, C. Ańe, O. Eulenstein, D. Ferńandez-Baca, J. Kim, M.M. McMahon, and R. Piaggio-Talice, Fragmentation of large data sets in phylogenetic analyses, In: Reconstructing Evolution: New Mathematical and Computational Advances, Mike Steel and Olivier Gascuel, Eds., Oxford University Press, Oxford, (2007) pp. 199-216.
17. Sanderson M.J., Driskell A.C.: The challenge of constructing large phylogenetic trees. Trends Plant Sci. 8, 374-379 (2003).
18. Sanderson M.J., Purvis A., Henze C.: Phylogenetic supertrees: assembling the trees of life. Trends Ecol. Evol. 13(3), 105-109 (1998).
19. Semple C., Steel M.: Phylogenetics. Oxford University Press, New York (2003).
20. Steel M.: The complexity of reconstructing trees from qualitative characters and subtrees. J. Classification 9, 91-116 (1992).