Motivation: Multiple sequence alignment is a key problem to most bioinformatics applications, from evolutionary studies to prediction of protein structure, molecular function, intermolecular interactions, gene finding and phylogenitic analysis. The last ten years have witnessed a big improvement to existing multiple alignment tools and the development of new ones. Varieties of parallel architectures have been experimented such as supercomputer, cluster, grid, cloud, and multi-core machine for the purpose of reaching the highest level of accuracy and speed. Results: This paper surveys most popular tools to clarify how parallelism accelerates the processing of large biological data set and improve alignment accuracy. It also introduces a comparative study that aims at guiding biologists to choose the appropriate software depending on their requirements and their hardware potentials.