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(seq1, seq2[, proportion])	Compute the Hamming distance between two sequences.
pdist(seq1, seq2)	Calculate the p-distance between two aligned sequences.
logdet(seq1, seq2[, pseudocount])	Calculate the LogDet distance between two aligned sequences.
paralin(seq1, seq2[, pseudocount])	Calculate paralinear distance between two aligned sequences.
kmer_distance(seq1, seq2, k[, overlap])	Compute the k-mer distance between a pair of sequences.

Nucleotide distance metrics

jc69(seq1, seq2)	Calculate the JC69 distance between two aligned nucleotide sequences.
f81(seq1, seq2[, freqs])	Calculate the F81 distance between two aligned nucleotide sequences.
k2p(seq1, seq2)	Calculate the K2P distance between two aligned nucleotide sequences.
f84(seq1, seq2[, freqs])	Calculate the F84 distance between two aligned nucleotide sequences.
tn93(seq1, seq2[, freqs])	Calculate the TN93 distance between two aligned nucleotide sequences.