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

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(l2k) 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(22klk).

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