Large Parsimony

Even after having solved the problem of small parsimony, we still have a long way to go, because the final goal is to find the optimal phylogeny, not just the optimal internal labeling of a given phylogeny:

Problem 9.6   Large Parsimony.
INPUT: A matrix M describing m characters of a set of n species,
QUESTION: What is the optimal phylogeny for these species, i.e., the one minimizing the parsimony score?

Again, this problem has a weighted and a non-weighted (discrete) version, but the difference is not essential. It can be shown that this problem is NP-hard. However, all is not lost. We will present several algorithms attempting to solve the problem of large parsimony.