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An improved algorithm for statistical alignment of sequences related by a star tree

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Abstract

The insertion-deletion model developed by Thorne, Kishino and Felsenstein (1991, J. Mol. Evol., 33, 114–124; the TKF91 model) provides a statistical framework of two sequences. The statistical alignment of a set of sequences related by a star tree is a generalization of this model. The known algorithm computes the probability of a set of such sequences in O(l 2k) time, where l is the geometric mean of the sequence lengths and k is the number of sequences. An improved algorithm is presented whose running time is only O(22k l k).

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Author notes

  1. István Miklós

    Present address: Collegium Budapest, Institute for Advanced Study, Szenthároms’ag utca 2, H-1014, Budapest, Hungary

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  1. Department of Plant Taxonomy and Ecology, Eötvös Loránd University, Pázmány Péter sétány 1/c, H-1117, Budapest, Hungary

    István Miklós

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  1. István Miklós
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Miklós, I. An improved algorithm for statistical alignment of sequences related by a star tree. Bull. Math. Biol. 64, 771–779 (2002). https://doi.org/10.1006/bulm.2002.0300

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  • DOI: https://doi.org/10.1006/bulm.2002.0300

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