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Bioinformatics Vol. 19 Suppl. 1 2003
Pages i147-i157
© 2003 Oxford University Press

Using guide trees to construct multiple-sequence evolutionary HMMs

I. Holmes

Department of Statistics, University of Oxford. 1 South Parks Road, Oxford OX1 3TG, UK

Received on January 6, 2003 ; accepted on February 20, 2003

Motivation: Score-based progressive alignment algorithms do dynamic programming on successive branches of a guide tree. The analogous probabilistic construct is an Evolutionary HMM. This is a multiple-sequence hidden Markov model (HMM) made by combining transducers (conditionally normalised Pair HMMs) on the branches of a phylogenetic tree.

Methods: We present general algorithms for constructing an Evolutionary HMM from any Pair HMM and for doing dynamic programming to any Multiple-sequence HMM.

Results: Our prototype implementation, Handel, is based on the Thorne-Kishino-Felsenstein evolutionary model and is benchmarked using structural reference alignments.

Availability: Handel can be downloaded under GPL from www.biowiki.org/Handel


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