Class Specialization
N2 AFScore
N2 computes the inner product of the standardised neighbourhood kmer count vectors

AFScore

N2 AFScore

AFScore<N2>
Include Headers
seqan/alignment_free.h
Remarks
N2 can be used for alignment-free sequence comparison.
Specialization of
AFScore
Data Members

bgModelOrder | Order of the background model
kmerSize | Size of the kmers
mismatches | Approximate word matches [0(exact)/1(one mismatch)]
mismatchWeight | Weight for approximate word matches
outputFile | When specified, all kmerWeights for every sequence will be written to this file
revCom | Scoring of reverse complements words [''/'max'/'min'/'mean'/'both_strands'/]

Member Functions

AFScore | Constructor

Functions

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

SeqAn - Sequence Analysis Library - www.seqan.de

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