# Analysis with Profile Hidden Markov Models

## Documentation for package ‘aphid’ version 1.3.3

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

## Help Pages

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.