It is sequence analysis tool

1. Multiple Sequence Alignment

2.  Multiple Sequence Alignment(MSA) is generally
the alignment of three or more biological sequence
(Protein or Nucleic acid) of similar length.
 From the output, homology can be inferred and the
evolutionary relationship between the sequence
studied.

3. Dynamic Programming approach
Progressive method
Iterative method

4.  In fact, dynamic programming is applicable to
align any number of sequences.
 Computes an optimal alignment for a given
score function.
 Because of its high running time, it is not
typically used in practice.

6.  In this method, pairwise global alignment is
performed for all the possible and these pairs are
aligned together on the basis of their similarity.
 The most similar sequences are aligned together
and thenless related sequences are added to it
progressively one-by-one until a complete
multiple query set is obtained.
 This method is also called hierarchical method
or tree method

9.  A method of performing a series of steps to produce
sucessively better approximation to align many
sequences step-by-step is called iterative method.
 Here the pairwise sequence alignment is totally
avoided.
 Iterative methods attempt to improve on the weak
point of the progressive methods the heavy
dependence on the accuracy of the initial pairwise
alignment.

11.  Clustal W
 Clustal W2
 Clustal Omega
 Kalign
 MAFFT
 MUSCLE
 M View
 T-Coffee
 Web PRANK
 MEME
 MACAW

12.  Detecting similarities between sequences(closely or
distinctly related).
 Detecting conserved regions or motifs in sequences.
 Detecting of structural homologies.
 Thus, assisting the improved prediction of secondary and
tertiary structures of proteins.