We have introduced the concept, statistical background, and databases used for sequence alignment. In addition to pairwise sequence alignment, multiple sequence alignments (MSA) provide a lot of information that can be used to predict the structure and function of nucleotide or protein sequence families. The structure and function of proteins constrain the evolution of the sequences. Regions that are important for protein structure and function accumulate changes more slowly because selection tends to remove individuals with nonfunctional proteins from the population (assuming a protein that affects fitness). MSA therefore gives powerful clues to where the important functional regions of the protein lie. We have already learned how to select sequences using BLAST and UniProt, we will use these selected sequences to construct a multiple sequence alignment in this chapter.