Viterbi                 The Viterbi algorithm.
align                   Multiple sequence alignment in R.
aphid                   The 'aphid' package for analysis with profile
                        hidden Markov models.
backward                The backward algorithm.
casino                  Dishonest casino.
deriveHMM               Derive a standard hidden Markov model from a
                        set of sequences.
derivePHMM              Derive a profile hidden Markov model from
                        sequences.
forward                 The forward algorithm.
generate                Generate random sequences from a model.
globins                 Globin protein alignment.
logsum                  Sum of logged probabilities.
map                     Optimized profile HMM construction.
plot.HMM                Plot standard hidden Markov models.
plot.PHMM               Plot profile hidden Markov models.
posterior               Posterior decoding.
print                   Print summary methods.
readPHMM                Import profile hidden Markov models into R.
substitution            Substitution matrices.
train                   Iterative model refinement.
unalign                 Deconstruct an alignment.
weight                  Sequence weighting.
writePHMM               Export profile hidden Markov models as text.