I have a fasta file with amino acid sequences. Now I want to align every sequence with every other (so it's pairwise). The outcome should be a distance (or similarity, doesn't matter) matrix.
I would like to do local alignment. EDIT: The sequences do NOT have the same length and might just have similar regions partially.
What tool would you suggest?
Ideally I can later do the same with nucleotide sequences.
This solution expects all seqs to be the same length, right?
Yes. To compare distances they must be aligned.