Why to Performing Multiple Alignments?

Multiple nucleotide or amino acid sequence alignment techniques are usually motivated by one of the following goals:

• Characterization of protein families, or identification of shared regions of homology in a multiple sequence (this may happen when a sequence search revealed homologies to several sequences)
• Determination of the consensus sequence of several aligned sequences.
• Help predicting the secondary and tertiary structures of new sequences.
• Preliminary step in molecular evolution analysis using phylogenetic methods for constructing phylogenetic trees.