Multiple sequence alignment.

A multiple sequence alignment, or multiple alignment, is a generalization of the case of 2 sequences to k sequences. Instead of relating the sequences by a single parent, we have an EPT which describes the parent-descendant relations. Dynamic programming is no longer applicable in practice, it requires exponential space and time in k. The following is an example of a multiple sequence alignment with k=5 for the sequences described in the earlier examples.

  1     FKQCCWNSLP____RGLSNVALVYQEFMAKCRGESENLQLVTALVINLPSMA
  2   SMFRQCIWNSLS____HGLPETAPIYQPLKARCRGVSENLQLVTEIIINLPTLC
  3   SLWCQCIKASLPLKVIRGTPEVAPLYDQLEQVCRSENQ____VSEIVAKFASLC
  4   TMFKMCLWNALP____RGLPEVAPVYRPLKARCRGDSENLQLCAERLVNLPELC
  5   AILRSCIWNLLP____RGLPEAAPIYEPLKARLRGESENYKLVTEIIMTLPSLC