Sequence distance metrics (skbio.sequence.distance)

This module provides functions for computing distances between biological sequences. These functions can be used directly on two Sequence objects, or supplied to other parts of the scikit-bio API that accept a sequence distance metric as input, such as align_dists, Sequence.distance, and PairwiseMatrix.from_iterable.

Generic distance metrics

hamming	Compute the Hamming distance between two sequences.
pdist	Calculate the p-distance between two aligned sequences.
logdet	Calculate the LogDet distance between two aligned sequences.
paralin	Calculate paralinear distance between two aligned sequences.
kmer_distance	Compute the k-mer distance between a pair of sequences.

Nucleotide distance metrics

jc69	Calculate the JC69 distance between two aligned nucleotide sequences.
f81	Calculate the F81 distance between two aligned nucleotide sequences.
k2p	Calculate the K2P distance between two aligned nucleotide sequences.
f84	Calculate the F84 distance between two aligned nucleotide sequences.
tn93	Calculate the TN93 distance between two aligned nucleotide sequences.