[R] R package for computing state path using Viterbi algorithm

Spencer Graves spencer.graves at pdf.com
Mon Mar 27 05:04:52 CEST 2006

	  Have you tried www.bioconductor.org?

	  If you are studying nucleatide sequences, I would think you might get 
better help from Bioconductor.  If you've already tried that (and you 
haven't received replies I've missed), it looks like you've found an 
opportunity to develop new code.

	  I hope that this relatively negative reply is better than the none 
that I've seen.

	  best wishes,
	  spencer graves

Wuming Gong wrote:

> Dear list,
> This question is about Hidden Markov Model.  Given a transition
> matrix, an emission matrix and a sequence of observed symbols
> (actually, nucleotide sequences, A, T, C and G), I hope to predict the
> sequence of state by Viterbi algorithm.  I searched R repository for
> related packages.  msm package has function viterbi.msm (as well as
> very good document), but it only works for continuous-time condition. 
> Other two HMM related packages, hmm.discnp and repeats, however, does
> not have such a function (similar to "hmmviterbi()" function in
> MatLab).
> Is there an R package that implements such a function?
> Thanks,
> Wuming
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