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This approach begins with the alignment
of the two most closely related sequences (as determined by
pairwise analysis) and subsequently adds the next closest
sequence or sequence group to this initial pair
[37,7]. This process
continues in an iterative fashion, adjusting the positioning of
indels in all sequences.
The major shortcoming of this approach is that a bias may be
introduced in the inference of the ordered series of motifs
(homologous parts) because of an overrepresentation of a subset of sequences.