I've googled around a bit. From reading the publications and software documentation, its clear that there is a distance matrix being used but it doesnt seem possible to obtain. There is rumor of a --distout flag that may produce a matrix, but the authors have said its for their purposes only and its not a real distance matrix, it's something else. (see: Mafft Output Distance Matrix).

Anyway, just wondering then how anyone here would go about computing a matrix from a MAFFT alignment if they had to. (Would it be appropriate to use another tool with a different scoring method to generate one, such as emboss dismat??)