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

Wuming Gong wuming.gong at gmail.com
Wed Mar 22 16:18:54 CET 2006

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

Is there an R package that implements such a function?



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