In practice, doesn't give optimal alignment. But were close Seems reasonable that the optimal alignment won't be far from the diagonal we were on, so we just set bounds on the location of the msa within the cube based on each pairwise-alignment Then just do dynamic programing within the volume defined by the pre-imposed boundsIn practice, doesn’t give optimal alignment…But we’re close! Seems reasonable that the optimal alignment won’t be far from the diagonal we were on…so we just set bounds on the location of the msa within the cube based on each pairwise-alignment. Then just do dynamic programing within the volume defined by the pre-imposed bounds