idea: multiple linkage clustering

http://wwwsup.scmbb.ulb.ac.be/~ocha/wwwsup1/help/sofist.paper.html

This paper use a tree like graph (multiple linkage clustering) to show align distances.
It's a pretty good idea which let you decide how many and where you want to align.
And also the way it shows the result is pretty good, it can show you the main core, the difference of those sequences.