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

Research output: Contribution to journalArticle

9 Citations (Scopus)

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(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).

Original languageEnglish
Pages (from-to)771-779
Number of pages9
JournalBulletin of Mathematical Biology
Volume64
Issue number4
DOIs
Publication statusPublished - Jul 2002

Fingerprint

Sequence Alignment
sequence alignment
Stars
Star
Alignment
statistical models
Geometric mean
Deletion
Insertion
alignment
Model

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

An improved algorithm for statistical alignment of sequences related by a star tree. / Miklós, I.

In: Bulletin of Mathematical Biology, Vol. 64, No. 4, 07.2002, p. 771-779.

Research output: Contribution to journalArticle

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