A Cluster Reduction for Computing the Subtree Distance Between Phylogenies

Annals of Combinatorics

Volumn 15, Issue 3, 2011, Pages 465-484

  Linz, Simone ^a   Semple, Charles ^b  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

cluster reduction; phylogenetic tree; subtree prune and regraft

Indexed keywords

EID: 80052968496     PISSN: 02180006     EISSN: 02193094     Source Type: Journal    
DOI: 10.1007/s00026-011-0108-3     Document Type: Article

References (15)

1. Allen B. L., Steel M.: Subtree transfer operations and their induced metrics on evolutionary trees. Ann. Combin. 5(1), 1-15 (2001).
2. Ávila L. F., García G., Serna M., Thilikos D. M.: A list of parameterized problems in bioinformatics. Technical report LSI-06-24-R. Technical University of Catalonia, Catalonia (2006).
3. Baroni M., Semple C., Steel M.: A framework for representing reticulate evolution. Ann. Combin. 8(4), 391-408 (2004).
4. Baroni M., Grünewald S., Moulton V., Semple C.: Bounding the number of hybridization events for a consistent evolutionary history. J. Math. Biol. 51(2), 171-182 (2005).
5. Baroni M., Semple C., Steel M.: Hybrids in real time. Syst. Biol. 55(1), 46-56 (2006).
6. Beiko, R., Hamilton, N.: Phylogenetic identification of lateral genetic transfer events. BMC Evol. Biol. 6, #15 (2006).
7. Bordewich M., Semple C.: On the computational complexity of the rooted subtree prune and regraft distance. Ann. Combin. 8(4), 409-423 (2004).
8. Bordewich M., Linz S., John K. St., Semple C.: A reduction algorithm for computing the hybridization number of two trees. Evol. Bioinform. Online 3, 86-98 (2007).
9. Downey R., Fellows M.: Parameterized Complexity (Monographs in Computer Science). Springer Verlag, New York (1999).
10. Gramm J., Nickelsen A., Tantau T.: Fixed-parameter algorithms in phylogenetics. Comput. J. 51(1), 79-101 (2008).
11. Hillis D. M., Moritz C., Mable B. K.: Molecular Systematics. Sinauer Associates, Massachusetts (1996).
12. Maddison W.: Gene trees in species trees. Syst. Biol. 46(3), 523-536 (1997).
13. Nakhleh L., Warnow T., Linder C. R., John K. St.: Reconstructing reticulate evolution in species -theory and practice. J. Comput. Biol. 12(6), 796-811 (2005).
14. Semple C., Steel M.: Phylogenetics. Oxford University Press, Oxford (2003).
15. Song, Y., Hein, J.: Parsimonious reconstruction of sequence evolution and haplotype blocks: finding the minimum number of recombination events. In: Algorithms in Bioinformatics, Lecture Notes in Bioinformatics, Vol. 2812, pp. 287-302. Third International Workshop, Budapest (2003).