5. The MSA program

Carrillo and Lipman boundary:
  • Projection of the MSA into series of pairwise alignments
  • Assumption: It is not necessary to compute all the combinations
  • Every pairwise alignment defines a set of spatial positions within which the optimal MSA is suposed to be (heuristic)

MSA procedure:

  1. Calculate all pairwise alignments and associated distances
  2. Use the distances to build a trial phylogenetic tree
  3. Calculate pair weights based on the tree (divergence among sequences)
  4. Produce a heuristic MSA based on the tree
  5. From alignments and the heuristic MSA, determine the relevant positions
  6. Perform the optimal alignment (SP-score) within the relevant space