Spec D2Star AFSScore
D2Star computes the inner product of the standardised kmer count vectors.

Extends AFScore
All Extended AFScore
Defined in <seqan/alignment_free.h>
Signature template <> struct AFScore<D2Star>;

Member Function Overview

Member Variable Overview

Detailed Description

D2Star can be used for alignment-free sequence comparison, this version calculates the background model on the concatenation of both sequences


Reinert, G.; Chew, D.; Sun, F., Waterman, M. S. Alignment-Free Sequence Comparison (I): Statistics and Power. J Comput Biol, 2009.

See Also

Member Functions Detail

AFScore::AFScore(kmerSize, bgModelOrder, verbose);



kmerSize Size of kmer, unsigned.
bgModelOrder Order of the background Markov model, unsigned.
verbose This option will report progress to standard output, bool.

Member Variables Detail

unsigned D2StarAFScore::bgModelOrder

Order of the background model.

unsigned D2StarAFScore::kmerSize

Size of the kmers.

CharString D2StarAFScore::outputFile

When specified, all kmerWeights will be written to this file, for every sequence, and for every sequence comparison.