Generalized Pair Hidden Markov Chain Model for Sequence Alignment

calculategphmm | Calculate GPHMM probability. |

computeCounts | Compute counts for emissions and transitions. |

computegphmm | Compute GPHMM log probability. |

computeGphmmParam | Compute gphmm parameters from counts. |

generateRandomSequences | Split randomly any R object for which method length() has... |

generateRead | Generate a noisy read from a true sequence. |

initializeGphmm | Initial parameters for gphmm. |

makeGphmmPerRead | Create a function to compute gphmm probabilities during the... |

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