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.

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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.

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