Sequence distance metrics (skbio.sequence.distance)#

This module contains functions for computing distances between scikit-bio Sequence objects. These functions can be used directly or supplied to other parts of the scikit-bio API that accept a sequence distance metric as input, such as skbio.sequence.Sequence.distance() and skbio.stats.distance.DistanceMatrix.from_iterable().


hamming(seq1, seq2)

Compute Hamming distance between two sequences.

kmer_distance(seq1, seq2, k[, overlap])

Compute the kmer distance between a pair of sequences.