Multiple Sequence Alignment(MSA) is a biological concept of aligning three or more sequences. It is of great importance for studying the genetic functions, structures and evolution process of the biological sequences. The aligning of multiple sequences is one of the most fundamental problems in Bioinformatics and it has been widely used for a lot of biological applications like predicting the shapes of proteins, constructing the phylogeny trees, etc . MSAs demand extremely sensitive computational methodologies to come up with precise results. The objective of this project is to conduct a comparative study on various MSA tools on the basis of computation time, accuracy, memory use and sequence length to identify the best use-case for each.