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# skbio.sequence.distance.kmer_distance

`skbio.sequence.distance.``kmer_distance`(seq1, seq2, k, overlap=True)

  Compute the kmer distance between a pair of sequences

  State: Experimental as of 0.5.0.

  The kmer distance between two sequences is the fraction of kmers that are unique to either sequence.

  Parameters:

  - seq2 (seq1,) – Sequences to compute kmer distance between.
  - k (int) – The kmer length.
  - overlap (bool, optional) – Defines whether the kmers should be overlapping or not.

  Returns: | kmer distance between seq1 and seq2.
  Return type: | float

  Raises:

  - `ValueError` – If k is less than 1.
  - `TypeError` – If seq1 and seq2 are not `Sequence` instances.
  - `TypeError` – If seq1 and seq2 are not the same type.

  Notes

  kmer counts are not incorporated in this distance metric.

  `np.nan` will be returned if there are no kmers defined for the sequences.

  Examples

      >>> from skbio import Sequence
      >>> seq1 = Sequence('ATCGGCGAT')
      >>> seq2 = Sequence('GCAGATGTG')
      >>> kmer_distance(seq1, seq2, 3) # doctest: +ELLIPSIS
      0.9230769230...