BIBI uses clustalw  for this construction. This is a basic way to do, more
sophisticated/complicated have been tested but this one appears convenient
for the general use.
The method used is the NJ (Neighbour Joining) method of Saitou and Nei. First
you calculate distances (percent divergence) between all pairs of sequence
from a multiple alignment; second you apply the NJ method to the distance
You can import the alignment from BIBI (see at the bottom of the result page) to
compute some other trees types.