If you have access to a UNIX machine, you should consider the MSA
program, which should be available from Stephen Altschul at the NCBI/NLM.
%A D. J. Lipman
%A S. F. Altschul
%A J. D. Kececioglu
%T A tool for multiple sequence alignment
%J Proc. Natl. Acad. Sci. USA
This program works well for up to about 5 sequences of 200 residues if they
are > 25% identical. It does a rigorous alignment.
I would be very cautious about successive pairwise alignment schemes,
such as the Feng-Doolittle method (Pileup) and Clustal. Any multiple
alignment method, including MSA, can do well on sequences with very
few gaps. The reason you need a multiple alignment is to rationally
place gaps based on the information from several sequences. Pairwise
schemes can have serious problems in appropriately weighting large
gaps in multiple alignments. I am familiar with one Feng-Doolittle
tree in the literature which is very unlikely to be correct, because
most of the topology was defined by gap weights.