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.

Data Races

If not stated otherwise, concurrent invocation is not guaranteed to be thread-safe.

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.