There are several servers out there to perform the multiple sequence alignment and visualization. I was looking for all in one offline tool to perform the multiple sequence alignment and generate a publication quality image. We can use msa package for both amino acid and DNA alignment. Following Rscript can be used for this purpose. Script is heavily commented to easy understand.Hope it will be helpful for others too.

Sequence Similarity Search - I : Basic Local Alignment Search Tool (BLAST) HERE