Cedric Notredame's T-Coffee can do that. In fact that's how it works: it builds pairwise alignments of all possible pairs (you can also use only a few or many alternative ones) and turns them into a so-called library. That gets checked for consistency, extended through triplet comparisons etc. and from there a multiple alignment is build.
The procedure to use your own pairwise alignments as input should be described in the T-Coffee manual