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Difference between Pairwise and Multiple Sequence Alignment

Sequence alignment is used to find out degrees of similarity between two (pairwise alignment)or more nucleic acid sequences of DNA or RNA and amino acid sequences of proteins.
Pair wise alignment vs Multiple sequence alignment

Pairwise Alignment vs Multiple Sequence Alignment
Pairwise Alignment
Multiple Sequence Alignment (MSA)
An alignment procedure comparing two biological sequences of either protein, DNA or RNA           
An alignment procedure comparing three or more biological sequences of either protein, DNA or RNA
Pairwise alignments can be generally categorized as global or local alignment methods.
MSA is generally a global multiple sequence alignment
Comparatively simple algorithm is used
Complex sophisticated algorithm is used
A general global alignment technique is the Needleman–Wunsch algorithm.
A general local alignment method is Smith–Waterman algorithm.
A technique called progressive alignment method is employed. In this approach, a pairwise alignment algorithm is used iteratively, first to align the most closely related pair of sequences, then the next most similar one to that pair, and so on.
Applications:

a) Primarily to find out conserved regions between the two sequences.

b)Similarity searches in a database

Applications:
a) To detect regions of variability or conservation in a family of proteins
b) Phylogenetic analysis (inferring a tree, estimating rates of substitution, etc.)
c) Detection of homology between a newly sequenced gene and an existing gene family prediction of protein structure
d) Demonstration of homology in multigene families
Examples of pairwise alignment  tools:
  • LALIGN
  • BLAST
  • EMBOSS Needle
  • EMBOSS Water
Examples of Multiple Sequence Alignment tools:
  • MUSCLE
  • T-Coffee
  • MAFFT
  • CLUSTALW 

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