Dear David Roe,
I am not really sure what you mean by 'the same scale', but I assume for now multiple aligned sequences... if you mean you want to align multiple sequences, you could use the sequence alignment function.
For example:
HIVseqs = multialignread('aagag.aln');
showalignment(HIVseqs)
Or something like:
seqalignviewer('aagag.aln')
Here is the accompanying documentation: seqalignviewer, which requires as input multiple aligned sequences from multialign. Or you could use showalignment to have a look at your multiple sequences.
