Compute a pairwise SNP distance matrix from a DNA alignment

Counts the number of nucleotide differences between every pair of sequences, via ape::dist.dna() with model "N".

Usage

get_snp_dist_matrix(dna_aln, core = TRUE)

Arguments

dna_aln

A DNA alignment object of class DNAbin.

core

Logical; if TRUE, sites with missing data in any sequence are dropped before counting, giving a core-genome distance. If FALSE, missing data are handled per pair of sequences (pairwise deletion).

Value

A numeric matrix of pairwise SNP distances between sequences.