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Bioinformatics. 2003;19 Suppl 1:i147-57.

Using guide trees to construct multiple-sequence evolutionary HMMs.

Author information

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

Abstract

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.

PMID:
12855451
[PubMed - indexed for MEDLINE]
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