Analysis with Profile Hidden Markov Models

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Documentation for package ‘aphid’ version 1.3.5

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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.