Parallelization of the AAE algorithm

The exact algorithm formulated by Kececioglu and Starrett (2004) provides a solution to the NP-complete problem of aligning alignments in most biological cases. This work investigates potential speedups that may be gained through the parallelization of the dynamic programming phase of this particular algorithm. Results indicate it is possible to improve the run time performance of the algorithm over non-trivial alignments that compose to a matrix of greater than 10^5 cells.