Abstract
In this paper some of the most fundamental problems in computational biology are proved intractable. The following problems are shown NP-hard for all binary or larger alphabets under all fixed metrics: Multiple Alignment with SP-score, Star Alignment, and Tree Alignment (for a given phylogeny). Earlier these problems have only been shown intractable for sporadic alphabets and distances, here the intractability is settled. Moreover, the construction can be extended to prove NP-hardness results for Consensus Patterns and Substring Parsimony.
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Elias, I. (2003). Settling the Intractability of Multiple Alignment. In: Ibaraki, T., Katoh, N., Ono, H. (eds) Algorithms and Computation. ISAAC 2003. Lecture Notes in Computer Science, vol 2906. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-24587-2_37
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DOI: https://doi.org/10.1007/978-3-540-24587-2_37
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-20695-8
Online ISBN: 978-3-540-24587-2
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