Phylogenetic Trees and Multiple Alignments
Iterative alignment strategy
The aim is to reduce the problem of a multiple alignment to an iteration of pairwise alignments.
The procedure works as follows:
The bottom up alignment requires comparing groups of pre-aligned sequences. This is achieved by using profile alignment. Profile alignment relies on a NW like algorithm, however with scores defined as average scores among columns of pre-aligned sequence groups.
Again the concept of the edit matrix is used to obtain a dynamic programming algorithm. A possibility to treat the gaps in profile alignments is to look into the profiles and to overtake gap-penalties to the edit matrix.
Advantages of iterative alignment procedure:
Comments are very welcome.