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. |