Performance Comparison of MPI-Based Parallel Multiple Sequence Alignment Algorithm Using Single and Multiple Guide Trees

Multiple alignment of biological sequences is an interesting area of research for application of parallel processing algorithms. For multiple alignment of sequences, parallelism can be introduced at different levels to reduce the overall time. This paper is concerned with the comparison of an MPI-based multiple sequence alignment algorithm by using single and multiple guide trees. In this work, we will look at the application of divide-and-conquer algorithm for multiple sequence alignment and discuss two different implementations on MPI. We compare the speed up of the two approaches and we contrast the quality of the alignments for these two approaches. These two approaches differ in using one single tree for alignment vs. multiple trees for alignment that we further discuss in this paper