9. T-coffee

  1. Generate a primary library of global and local pairwise alignments
  2. For each pair of residue matches assign a weight depending on the identity of both sequences
  3. Combination of information: merge duplicated pairs in the library adding their weights (signal addition)
  4. 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).
  5. Progressive alignment: neighbour-joining method. The matrix of substitutions will be the extended library. No gap penalties.