Iterative pairwise alignment

This approach uses pairwise alignment scores to iteratively add one additional string to a growing multiple alignment. We start by aligning the two strings whose edit distance is the minimum over all pairs of strings. Then we iteratively consider the string with the smallest distance to any of the strings already in the multiple alignment. More generally, the algorithm works as follows:

1.

Align some pair.

2.

while (not done)

(a)

Pick an unaligned string which is "near" some aligned one(s).

(b)

Align with the profile of the previously aligned group
Resulting new spaces are inserted into all strings in the group.