If you'd rather keep your original MSAs you can use the profile alignment option available in T-coffee.
There's a short bit of documentation here that describes the method.
Essentially you can just run the following command in a terminal:
$ t_coffee -profile=msa01.aln,msa02.aln -outfile=combined_msas.aln
I think clustal might have a similar function but t-coffee does lots of extra bits.
Hope that helps :)
Hi, you run a range of different MSA alignments in Jalview. It allows multiple views of the same sequences that have been aligned by different methods. Jalview also has an option where sequences can be grouped and represented by single sequence. In theory it would be possible to then align these representative sequences and compare the results.