I am trying to compare 10 sequences (~1Mbp size each) to find out their divergence and phylo genetic tree. I am getting my phylo tree from MAFFT which provides the branch length in "substitution per site" unit. However, these branch lengths are by a factor of 10 higher than my results from pairwise BLAST comparison between the sequences.
Is there a justification for this? and if not, what are the alternatives to get corresponding results?