On the complexity of computing MP distance between binary phylogenetic   trees
  Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the difference of the parsimony scores of a single character on both trees under consideration, and the goal is to find the character which maximizes this difference. Here we show that computation of MP distance on two \emph{binary} phylogenetic trees is NP-hard. This is a highly nontrivial extension of an earlier NP-hardness proof for two multifurcating phylogenetic trees, and it is particularly relevant given the prominence of binary trees in the phylogenetics literature. As a corollary to the main hardness result we show that computation of MP distance is also hard on binary trees if the number of states available is bounded. In fact, via a different reduction we show that it is hard even if only two states are available. Finally, as a first response to this hardness we give a simple Integer Linear Program (ILP) formulation which is capable of computing the MP distance exactly for small trees (and for larger trees when only a small number of character states are available) and which is used to computationally verify several auxiliary results required by the hardness proofs. 
Steven Kelk and Mareike Fischer
q-bio.PE cs.CE cs.DS math.CO