Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL

Here we introduce the Optimal Tree Completion Problem, a general optimization problem that involves completing an unrooted binary tree (i.e., adding missing leaves) so as to minimize its distance from a reference tree on a superset of the leaves. More formally, given a pair of unrooted binary trees (T,t) where T has leaf set S and t has leaf set R, a subset of S, we wish to add all the leaves from S R to t so as to produce a new tree t\u27 on leaf set S that has the minimum distance to T. We show that when the distance is defined by the Robinson-Foulds (RF) distance, an optimal solution can be found in polynomial time. We also present OCTAL, an algorithm that solves this RF Optimal Tree Completion Problem exactly in quadratic time. We report on a simulation study where we complete estimated gene trees using a reference tree that is based on a species tree estimated from a multi-locus dataset. OCTAL produces completed gene trees that are closer to the true gene trees than an existing heuristic approach, but the accuracy of the completed gene trees computed by OCTAL depends on how topologically similar the estimated species tree is to the true gene tree. Hence, under conditions with relatively low gene tree heterogeneity, OCTAL can be used to provide highly accurate completions of estimated gene trees. We close with a discussion of future research

Subtree weight ratios for optimal binary search trees

For an optimal binary search tree T with a subtree S(d) at a distance d from the root of T, we study the ratio of the weight of S(d) to the weight of T. The maximum possible value, which we call ρ(d), of the ratio of weights, is found to have an upper bound of 2/F_d+3 where F_i is the ith Fibonacci number. For d = 1, 2, 3, and 4, the bound is shown to be tight. For larger d, the Fibonacci bound gives ρ(d) = O(ϕ^d) where ϕ ~ .61803 is the golden ratio. By giving a particular set of optimal trees, we prove ρ(d) = Ω((.58578 ... )^d), and believe a similar proof follows for ρ(d) = Ω((.60179 ... )^d). If we include frequencies for unsuccessful searches in the optimal binary search trees, the Fibonacci bound is found to be tight

An efficient sampling algorithm for difficult tree pairs

It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees, (S, T), can be efficiently reduced to the problem of computing the rotation distance between a difficult pair of trees (S', T'), where there is no known first step which is guaranteed to be the beginning of a minimal length path. Of interest, therefore, is how to sample such difficult pairs of trees of a fixed size. We show that it is possible to do so efficiently, and present such an algorithm that runs in time O(n4)