Progressive Alignment:

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.