I am trying to get the proportion of sites that differ between each pair of sequences in my alignment. One approach would be: dist.dna from R package ape with model set as "raw" Another approach is dist.alignment from seqinr which gives the squared root of the pairwise distances. I hoped that the square of the values obtained using dist.alignment would be same as I got using dist.dna. But they are not
Does anyone know the reason for this difference, and which value should I trust?