PAC: Progressive Alignment with Consensus Sequences

is one of the major open problems in computational molecular biology. The purpose of this study was to provide a new method, PAC (Progressive Alignment with Consensus Sequences), for calculation of multiple amino acid sequence alignments. In PAC, multiple alignments are built by the successive application of pairwise alignment algorithms; the distance between two groups is defined as the distance between the two corresponding consensus sequences; group to group alignment is also calculated using the alignment of the consensus sequences. One advantage of PAC is that it is simple and efficient, and in many cases generates reasonable results. Another advantage of this method is that the scoring can be done with reference to the evolutionary tree, even though the tree structure itself may remain unknown.