An R package for correlated mutation analysis at both codon and amino acid levels.

Global functions | |
---|---|

AccPi_true | Source code |

AccPij_true | Source code |

CMA | Man page |

CMA-package | Man page |

Compute_C | Source code |

Compute_Results | Source code |

Compute_True_Frequencies | Source code |

ReturnW | Source code |

aaDCA.fasta | Source code |

aaDCA.sth | Source code |

aa_letter_to_binary_vec | Source code |

aa_msa_to_binary_matrix | Source code |

aa_seq_to_binary_vec | Source code |

aacodonDCA | Source code |

arrayC | Source code |

bp_link | Source code |

calc_APC | Source code |

calc_MIp | Source code |

calculate_mi_and_omes | Source code |

codonDCA.fasta | Source code |

codonDCA.sth | Source code |

codon_letter_to_binary_vec | Source code |

codon_msa_to_binary_matrix | Source code |

codon_seq_to_binary_vec | Source code |

compute_di | Source code |

compute_mu | Source code |

dca | Man page Source code |

getExcludedIndices.fasta | Source code |

getExcludedIndices.sth | Source code |

hammingdist | Source code |

mapkey | Source code |

read.stockholm.alignment | Source code |

return_alignment | Source code |

sampledHammingdist | Source code |

with_pc | Source code |

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