Maximum Parsimony Multiple Sequence Alignment

I have one question that I find awfully confusing to follow.

Maximum Parsimony Multiple Alignment Problem Given: A set of sequence S1,…,Sn, and a tree T with one leaf per sequence Find: The alignment of S1,…,Sn such that the parsimony score of the alignment on tree T is minimized. Here, for the purpose of computing the parsimony score of a given alignment column, we consider a gap as a fifth character, other than A, C, G, and T. Explain how to modify the progressive alignment algorithm seen in class to adapt it to the Maximum Parsimony Multiple Alignment Problem.

Can anyone explain what the heck it means by "parsimony score of alignment on tree T"?

• Hey, check this out! After reading that, know that tree alignment is the process of restructuring a phylogenetic tree such that it produces the most optimal evolutionary tree, provided certain biological concepts. So then, "parsimony score of alignment on tree T" describes the act of measuring how optimally structured a phylogenetic tree is. – Charles Oct 10 '17 at 14:45