The seed alignment is initially pairwise, and new sequences are added via pairwise comparisons to sequences in the seed. Thus, all steps involve pairwise sequence-sequence comparisons. This contrasts to Profile Mode where all the later steps involve profile refinement via sequence-profile comparisons.
Progressive alignment was used e.g. in the CLUSTAL program (Higgins & Sharp: Fast and sensitive multiple sequence alignments on a microcomputer. Comput. Appl. Biosci. 1989;5:151-3.).