
DP for global pairwise alignment 

DP for global multiple alignment 
n is the length of the sequences and k the number of sequences
Score of a MSA (total distance of a MSA):
 Naive method: For every column in k sequences, there are 2^{k}1
combinations
 Distance from a consensus
 Tree alignments
 Star alignments
 Sum of pairs (SPscore): The sum of the pairwise score between all
pairs of sequences in every column
