We work with a simple indel model, together with our evolutionary model, to generate a pairwise statistical alignment. For two sequences x and y, a set of seed parameters then gives us the probability p ij of each i th position x i being aligned with each j th position y j . We subsequently work with expected observations as opposed to actual ones. We iteratively calculate the alignment probabilities and the maximum likelihood estimates of evolutionary parameters, until we reach a given level of convergence. We also extend our methodology to a multiple pairwise method.