A pairwise alignment is done with two sequences. One sequence is written over the other and then overlapping element chains are noted. Repeated chains of elements in a sequence exist because they were a favorable evolutionary adaption. Not all chains are the same length and thus gaps and insertions must be noted in the pairwise alignment.
A multiple sequence alignment is similar to the pairwise alignment, but it uses more than two protein sequences. A multiple sequence alignment can sometimes be presented in a tree-shape fashion.
A structural alignment is a type of sequence alignment that compares the shape of two or more protein sequences. Unlike pairwise alignment and multiple sequence alignment (both of which are only concerned with the elements within the sequences), a structural alignment looks at the whole of the sequences as one individual unit. Structural alignments are not written out, but must be compared three-dimensionally.