This Article 
   
 Share 
   
 Bibliographic References 
   
 Add to: 
 
Digg
Furl
Spurl
Blink
Simpy
Google
Del.icio.us
Y!MyWeb
 
 Search 
   
Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony
January-March 2009 (vol. 6 no. 1)
pp. 118-125
Taoyang Wu, Queen Mary, University of London, London
Vincent Moulton, University of East Anglia, Norwich
Mike Steel, University of Canterbury, Christchurch
Given a set X of taxa, a phylogenetic X-tree T that is only partially resolved, and a collection of characters on X, we consider the problem of finding a resolution (refinement) of T that minimizes the parsimony score of the given characters. Previous work has shown that this problem has a polynomial time solution provided certain strong constraints are imposed on the input. In this paper we provide a new algorithm for this problem, and show that it is fixed parameter tractable under more general conditions.

[1] E. Althaus and R. Naujoks, “Computing Steiner Minimum Trees in Hamming Metrics,” Proc. 17th Ann. ACM-SIAM Symp. Discrete Algorithms (SODA '06), pp. 172-181, 2006.
[2] G. Blelloch, K. Dhamdhere, E. Halperin, R. Ravi, R. Schwartz, and S. Sridhar, “Fixed Parameter Tractability of Binary Near-Perfect Phylogenetic Tree Reconstruction,” M. Bugliesi, B. Preneel, V.Sassone, I. Wegener, eds., Proc. 33rd Int'l Colloquium Automata, Languages and Programming (ICALP '06), Part I, pp. 667-678, 2006.
[3] M. Bonet, M. Steel, T. Warnow, and S. Yooseph, “Better Methods for Solving Parsimony and Compatibility,” J. Computational Biology, vol. 5, no. 3, pp. 391-408, 1998.
[4] T. Bruen and D. Bryant, “A Subdivision Approach to Maximum Parsimony,” Annals of Combinatorics, vol. 12, pp. 45-51, 2008.
[5] W.H.E Day, “Computationally Difficult Parsimony Problems in Phylogenetics Systematics,” J. Theoretical Biology, vol. 103, pp. 429-438, 1983.
[6] J Felsenstein, Inferring Phylogenies. Sinauer Assoc., Inc., 2004.
[7] W. Fitch, “Toward Defining the Course of Evolution: Minimum Change for a Specified Tree Topology,” Systematic Zoology, vol. 20, pp. 406-416, 1971.
[8] L.R. Foulds and R.L. Graham, “The Steiner Problem in Phylogeny Is NP-Complete,” Advances in Applied Math., vol. 3, pp. 43-49, 1982.
[9] M.R. Garey and D.S. Johnson, Computers and Intractability: A Guide to the Theory of NP-Completeness. W.H. Freeman, 1979.
[10] J.A. Hartigan, “Minimum Mutation Fits to a Given Tree,” Biometrics, vol. 29, pp. 53-65, 1973.
[11] D. Huson, M. Steel, and J. Whitfield, “Reducing Distortion in Phylogenetic Networks,” Proc. Sixth Workshop Algorithms in Bioinformatics (WABI '06), pp. 150-161, 2006.
[12] R. Niedermeier, Invitation to Fixed-Parameter Algorithms. Oxford Univ. Press, 2006.
[13] O. Nomura, Z.H. Lin, Muladno, Y. Wada, and H. Yasue, “A SINE Species from Hippopotamus and Its Distribution among Animal Species,” Mammalian Genome, vol. 9, no. 7, pp. 550-555, 1998.
[14] A.M. Shedlock and N. Okada, “SINE Insertions: Powerful Tools for Molecular Systematics,” Bioessays, vol. 22, pp. 148-160, 2000.
[15] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[16] M. Steel and D. Penny, “Maximum Parsimony and the Phylogenetic Information in Multi-State Characters,” Parsimony, Phylogeny and Genomics, V. Albert, ed., pp. 163-178, Oxford Univ. Press, 2005.

Index Terms:
Combinatorial algorithms, Life and Medical Sciences
Citation:
Taoyang Wu, Vincent Moulton, Mike Steel, "Refining Phylogenetic Trees Given Additional Data: An Algorithm Based on Parsimony," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 1, pp. 118-125, Jan.-March 2009, doi:10.1109/TCBB.2008.100
Usage of this product signifies your acceptance of the Terms of Use.