Making the shortest-paths approach to sum-of-pairs multiple sequence alignment more space efficient in practice (extended abstract)

The MSA program, written and distributed in 1989, is one of the few existing programs that attempts to find optimal alignments of multiple protein or DNA sequences. MSA implements a branch-and-bound technique on a variant of Dijkstra's shortest paths algorithm to prune the basic dynamic programming graph. We have made substantial improvements in the time and space usage of MSA. On some runs, we achieve an order of magnitude reduction in space usage and a significant multiplicative factor speedup in running time. To explain these improvements, we give a much more detailed description of PISA than has been previously available.