Analysis with Profile Hidden Markov Models


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Documentation for package ‘aphid’ version 1.3.3

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aphid-package The 'aphid' package for analysis with profile hidden Markov models.
align Multiple sequence alignment in R.
align.AAbin Multiple sequence alignment in R.
align.default Multiple sequence alignment in R.
align.DNAbin Multiple sequence alignment in R.
align.list Multiple sequence alignment in R.
aphid The 'aphid' package for analysis with profile hidden Markov models.
backward The backward algorithm.
backward.HMM The backward algorithm.
backward.PHMM 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.
derivePHMM.AAbin Derive a profile hidden Markov model from sequences.
derivePHMM.default Derive a profile hidden Markov model from sequences.
derivePHMM.DNAbin Derive a profile hidden Markov model from sequences.
derivePHMM.list Derive a profile hidden Markov model from sequences.
forward The forward algorithm.
forward.HMM The forward algorithm.
forward.PHMM The forward algorithm.
generate Generate random sequences from a model.
generate.HMM Generate random sequences from a model.
generate.PHMM 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.
posterior.HMM Posterior decoding.
posterior.PHMM Posterior decoding.
print Print summary methods.
print.DPA Print summary methods.
print.HMM Print summary methods.
print.PHMM Print summary methods.
readPHMM Import profile hidden Markov models into R.
substitution Substitution matrices.
train Iterative model refinement.
train.HMM Iterative model refinement.
train.PHMM Iterative model refinement.
unalign Deconstruct an alignment.
Viterbi The Viterbi algorithm.
Viterbi.default The Viterbi algorithm.
Viterbi.HMM The Viterbi algorithm.
Viterbi.PHMM The Viterbi algorithm.
weight Sequence weighting.
weight.AAbin Sequence weighting.
weight.default Sequence weighting.
weight.dendrogram Sequence weighting.
weight.DNAbin Sequence weighting.
weight.list Sequence weighting.
writePHMM Export profile hidden Markov models as text.