Abstract
Phylogenies play a major role in representing the interrelationships among biological entities. Many methods for reconstructing and studying such phylogenies have been proposed, almost all of which assume that the underlying history of a given set of species can be represented by a binary tree. Although many biological processes can be effectively modeled and summarized in this fashion, others cannot: recombination, hybrid speciation, and horizontal gene transfer result in networks, rather than trees, of relationships.
In a series of papers, we have extended the maximum parsimony (MP) criterion to phylogenetic networks, demonstrated its appropriateness, and established the intractability of the problem of scoring the parsimony of a phylogenetic network. In this work we show the hardness of approximation for the general case of the problem, devise a very fast (linear-time) heuristic algorithm for it, and implement it on simulated as well as biological data.
The authors appear in alphabetical order.
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Jin, G., Nakhleh, L., Snir, S., Tuller, T. (2007). A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. In: Măndoiu, I., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2007. Lecture Notes in Computer Science(), vol 4463. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-72031-7_6
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DOI: https://doi.org/10.1007/978-3-540-72031-7_6
Publisher Name: Springer, Berlin, Heidelberg
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