In [[Bioinformatics]], multiple alignment can be used to study [[evolutionary]] relationships between sequences of [[proteins]] or [[genes]]. Since the changes between gene sequences due to evolution are incremental, genes with a common evolutionary origin (or their protein products) can be compared by aligning identical or similar [[residues]].
A '''multiple sequence alignment''' is a graphical representation where several DNA or protein sequences are ''aligned'' on top of each other so that [[residues]] likely to play equivalent roles in the aligned sequences occupy the same column.
The comparison of these related genesalignment may then be used to study, which regions of genes have been conserved, and which are sensitive to [[mutation]], over the years. This is very useful in designing experiments to test and modify the function of specific proteins, to predict the function and [[protein structure|structure of proteins]], and to identify new members of protein families.
The production of a protein sequence alignment is also a necessary step for the study of the [[phylogeny]] of a protein family and for [[protein ___domain]] discovery. Some methods of prediction of protein features work better with the protein sequence and its alignment to other sequences, than with the protein sequence alone.
==Multiple Sequence Alignment programs and techniques==
