- Generate a primary library of global and local pairwise alignments
- For each pair of residue matches assign a weight depending on the
identity of both sequences
- Combination of information: merge duplicated pairs in the library adding
their weights (signal addition)
- Extended library: individual alignment of each pair of sequences with
the rest of sequences to provide more consistency to residue matches appearing
in more than one pairwise alignment (triplet approach).
- Progressive alignment: neighbour-joining method. The matrix of
substitutions will be the extended library. No gap penalties.