Multiple Alignment

Multiple Sequence Alignment (MSA) is an alignment of 3 or more sequences such that each column of the alignment is an attempt to represent the evolutionary changes, including substitution, insertion, and deletion.
Alignment of protein sequences can reveal whether there is functional and evolutionary relationship between the sequences.
Consensus information retrieved from MSA is used for the design of specific DNA probes to identify other members of the same group or family of similar sequences in different organisms.
The consensus can be used as a query sequence in database searching program to find other sequence with a similar pattern.
MSA are starting points for phylogenetic analysis.
Once the MSA has been found the number or types of changes in the aligned sequence residues maybe used for a phylogenetic analysis.
Each column in the alignment predicts the mutation that occured at one site during the evolutionary changes of sequence family.
Within the columns are original characters that were present early as well as other derived characters that appeared later in evolutionary time.

MSA can be global or local.....
An alignment of 2 sequences can be global alignment of the entire sequences or a local alignment of locally conserved regions in these sequences. These two types of alignments are also used in MSA.
In a global MSA, pairwise alignment is extended to include 3 or more related sequences.
Local conservation of patterns in DNA sequences represents conserved regulatory information in genome.
These patterns maybe found by local MSA designed to search for these conserved domains.

Tools....
Two main tools are used for MSA
a) CLUSTALW
b) TCOFFEE