Kaikoura Information Processing Letters tree theorems : Computing the maximum agreement subtree

The Maximum Agreement Subtree Problem was posed by Finden and Gordon in 1985, and is as follows: given a set S={s,, sz,..., s,,} and two trees P and Q leaf-labelled by the elements of S, find a maximum cardinality subset S, of S such that PI S, = Q IS,. This problem arises in evolutionary tree construction, where different methods or data yield (possibly) different trees for the same species on which the trees agree. A superpolynomial time algorithm for finding a maximum agreement subtree of two binary trees was found by Kubicka et al. In this paper, we will present an 0(n4.5 log IZ + V> algorithm to determine the largest agreement subtree of two trees on n leaves, where V is the maximum number of nodes in the trees. For the case of trees of maximum degree k, there are two algorithms presented: one has running time 0(k!n2 + V) while the other has running time O(k2%z2 log n + V). These algorithms also apply when the trees are constrained to be rooted; in this case a maximum agreement subtree is also constrained to be rooted. Each of the algorithms we present can be modified to produce a maximum agreement subtree, rather than computing only the size. Thus, we can solve the search problem in the same running time as