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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.

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Index Terms:
Combinatorial algorithms, Life and Medical Sciences
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
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