General View of How the Programs Work:

The most practical and widely used method for multiple sequence alignment uses hierarchical extensions of pairwise alignments. The algorithm is as follows:

1.

Perform all pairwise comparisons between the sequences.

2.

Perform cluster analysis on the pairwise data to generate a cluster hierarchy. This hierarchy may have in the form of a binary tree or a simple ordering.

3.

Construct the multiple alignment by first aligning the most similar pair of sequences, then the next most similar pair and so on. Once an alignment of two sequences has been made, it remains fixed. Thus for a set of sequences A, B, C, D having aligned A with C and B with D the alignment of A, B, C, D is obtained by comparing the alignment of A and C with that of B and D using averaged scores at each aligned position.