Analysis with Profile Hidden Markov Models

align | Multiple sequence alignment in R. |

aphid | The 'aphid' package for analysis with profile hidden Markov... |

backward | The backward algorithm. |

casino | Dishonest casino. |

deriveHMM | Derive a standard hidden Markov model from a set of... |

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 summary methods. | |

readPHMM | Import profile hidden Markov models into R. |

substitution | Substitution matrices. |

train | Iterative model refinement. |

unalign | Deconstruct an alignment. |

Viterbi | The Viterbi algorithm. |

weight | Sequence weighting. |

writePHMM | Export profile hidden Markov models as text. |

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