nwalign and swalign functions

hi, are nwalign and swalign functions requiring the two sequences with same length?

when I run it with two sequences with different length,and although the both sequences are amino acids, I got:

??? Error using ==> nwalign Both sequences must be either amino acids or nucleotides.

[Loris Podevyn]

No, you can use it on sequences of different length.

The problem here is that you are comparing a sequence of nucleotides with a sequence of amino acids. These are not comparable on a seqdotplot.