Randomly permuting the training corpus did not change our results significantly, so we believe our results are not greatly dependent on the initial sequence order.
instead of assigning substitution costs, we compute the cost of aligning a word into a particular column, as follows:  the probability of feature j from class i occurring in column k is a simple maximumlikelihood estimate -count the number of times we have already aligned that feature in the column and divide by the number of sequences aligned.