Maybe the Align function of AiO (http://134.99.88.55/aio/) combined with
the master sequence option is what you want.
It will optimize all alignments to one 'master' sequence and the output can
be in pure text (ASCII) so you can manipulate further.
See the handbook (http://134.99.88.55/aio/manual.pdf) at page 35.
Christiaan
