For simplicity, suppose that I am penalising mismatches and gaps with -1 and adding a score +100 for each match. Does the optimum alignment of the three DNA sequences
with the total score S = 294 + 294 - 6 = 586? In this case I sum the alignment score for each of the three pairs.
Or does it equal to:
with the score 200 - 7 = 193? In this case I am rewarding only the matches that occured across all three sequences at the same time.
Which of the two scores are the common Multiple Sequence Alignment algorithms trying to optimise for? Or if both are valid, then which optimal alignment (i.e. with respect to which definition) is preferred if realistic reward/penalise values were used?