Class Specialization

N2 AFScore

N2 computes the inner product of the standardised neighbourhood kmer count vectors

N2 AFScore |

Include Headers

seqan/alignment_free.h

Remarks

N2 can be used for alignment-free sequence comparison.

Specialization of

Data Members

Order of the background model | |

Size of the kmers | |

Approximate word matches [0(exact)/1(one mismatch)] | |

Weight for approximate word matches | |

When specified, all kmerWeights for every sequence will be written to this file | |

Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/] |

Member Functions

Constructor |

Functions

Computes the pairwise similarity scores for a set of sequences (AFScore) |

SeqAn - Sequence Analysis Library - www.seqan.de