Reconstructing reticulate evolution in species - Theory and practice

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn 8, Issue , 2004, Pages 337-346

  Nakhleh, Luay ^a   Warnow, Tandy ^a,c   Linder, C Randal ^b  

^a University of Texas at Austin ^*  (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^c HARVARD UNIVERSITY   (United States)

Author keywords

Gene trees; Phylogenetic networks; Subtree prune and regraft

Indexed keywords

GENE TREES; PHYLOGENETIC NETWORKS; SPECIES NETWORK; SUBTREE PRUNE AND REGRAFT;

ALGORITHMS; COMPUTER SIMULATION; ERROR ANALYSIS; GENES; POLYNOMIALS; PROBLEM SOLVING; TREES (MATHEMATICS);

BIODIVERSITY;

EID: 2442436724     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (18)

1. B. Allen and M. Steel. Subtree transfer operations and their induced metrics on evolutionary trees. Annals of Combinatorics, 5:1-13, 2001.
2. D. Bryant and V. Moulton. NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. In R. Guigo and D. Gusfield, editors, Proc. 2nd Workshop Algorithms in Bioinformatics (WABI'02), volume 2452 of Lecture Notes in Computer Science, pages 375-391. Springer Verlag, 2002.
3. W.H.E. Day. Optimal algorithms for comparing trees with labeled leaves. Journal of Classification, 2:7-28, 1985.
4. S.B. Gabriel, S.F. Schaffner, H. Nguyen, J.M. Moore, J. Roy, B. Blumenstiel, J. Higgins, M. DeFelice, A. Lochner, M. Faggart, S.N. Liu-Cordero, C. Rotimi, A. Adeyemo, R. Cooper, R. Ward, E.S. Lander, M.J. Daly, and D. Altshuler. The structure of haplotype blocks in the human genome. Science, 296(5576):2225-2229, 2002.
5. D. Gusfield. Efficient algorithms for inferring evolutionary trees. Networks, 21:19-28, 1991.
6. D. Gusfield, S. Eddhu, and C. Langley. Efficient reconstruction of phylogenetic networks with constrained recombination. In Proceedings of Computational Systems Bioinformatics (CSB 03), 2003.
7. D. Harel and R.E. Tarjan. Fast algorithms for finding nearest common ancestors. SIAM Journal on Computing, 13(2):338-355, 1984.
8. J.G. Lawrence and H. Ochman. Reconciling the many faces of lateral gene transfer. Trends in Microbiology, 10:1-4, 2002.
9. C.R. Linder, B.M.E. Moret, L. Nakhleh, A. Padolina, J. Sun, A. Tholse, R. Timme, and T. Warnow. Phylogenetic networks: generation, comparison, and reconstruction. Technical Report TR-CS-2003-26, University of New Mexico. 2003.
10. W.P. Maddison. Gene trees in species trees. Systematic Biology, 46(3):523-536, 1997.
11. L. Nakhleh, J. Sun, T. Warnow, C.R. Linder, B.M.E. Moret. and A. Tholse. Towards the development of computational tools for evaluating phylogenetic network reconstruction method. In Proc. 8th Pacific Symposium on Biocomputing (PSB 03), pages 315-326, 2003.
12. R. Page and M.A. Charleston. Trees within trees: Phylogeny and historical associations. Trends in Ecology and Evolution, 13:356-359, 1998.
13. D. Posada and C. Wiuf. Simulating haplotype blocks in the human genome. Bioinformatics, 19(2):289-290, 2003.
14. H. Shimodaira and M. Hasegawa. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Molecular Biology and Evolution, 16:1114-1116, 1999.
15. L. Wang, K. Zhang, and L. Zhang. Perfect phylogenetic networks with recombination. Journal of Computational Biology. 8(1):69-78, 2001.
16. T. Warnow. Tree compatibility and inferring evolutionary history. Journal of Algorithms, 16:388-407, 1994.
17. K. Zhang and L. Jin. HaploBlockFinder: haplotype block analyses. Bioinformatics, 19(10):1300-1301, 2003.
18. D. Zwickl and D. Hillis. Increased taxon sampling greatly reduces phylogenetic error. Systematic Biology, 51(4):588-598, 2002.