Pairwise sequence alignment looks at where two protein strands overlap in elemental chains. This is accomplished by writing out the elements in the protein chain and then noting where there are similar elemental chains.
Multiple sequence alignment is similar to pairwise sequence alignment, but is done with more than two protein strands. A multiple sequence alignment is frequently written out in a tree shape to make overlaps between the strands clear, because there are fewer overlaps than in a pairwise sequence alignment
Unlike pairwise and multiple sequence alignments, a structural sequence alignment analyzes the entire structure of a protein strand. Structural sequence alignment must be visualized three-dimensionally.
The most common protein strands analyzed in the three types of sequence alignments are DNA and RNA strands, which are important for understanding how organisms evolve. Viruses can also be analyzed (especially in structural sequence alignment), which can lead to more effective vaccine creation.
Sequence alignment can also be used to analyze non-biological sequences, such as in language. This is done in the same fashion as pairwise sequence alignment, with two words written on top of each other and commonalities noted. Language sequence alignment is particularly useful in trying to find the etymology of words.