Class

Score

A scoring scheme.

Parameters

The value type. Default: int | |

The specializing type. Default: Simple Score |

Specializations

Edit distance scoring scheme. | |

Pam scoring matrices. | |

Scoring scheme for chaining that uses a special method for scoring the gaps between two fragments. | |

Scoring scheme for chaining that computes gap scores using manhattan distance. | |

A general scoring matrix. | |

Scoring scheme for chaining that set gap scores to 0 | |

Simple scoring scheme that has scores for matches, mismatches, opening gaps and extending gaps. |

Functions

Given a multiple alignment, this function calculates all kinds of alignment statistics. | |

Computes the best global alignment of the two sequences. | |

Computes the best local alignment of two sequences. | |

Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. Refines (i.e. cuts into smaller parts) a set of pairwise segment matches in such a way that none of the segments partly overlap. They are either identical (fully overlapping) or non-overlapping. | |

Computes multiple local alignments of two sequences. | |

The score for aligning two values according to a scoring scheme. | |

Computes the best local alignment of the (two) sequences given in align. | |

Computes next best local alignment. | |

Given a multiple alignment, this function calculates the sum-of-pairs score. |

Example Programs

SeqAn - Sequence Analysis Library - www.seqan.de