Approximation and Exact Algorithms for Constructing Minimum Ultrametric Trees from Distance Matrices

An edge-weighted tree is called ultrametric if the distances from the root to all the leaves in the tree are equal. For an n by n distance matrix M, the minimum ultrametric tree for M is an ultrametric tree T = (V, E, w) with leaf set {1,..., n} such that dT(i, j) ≥ M[i, j] for all i, j and $$\sum {_{e \in E} w(e)}$$ is minimum, where dT(i, j) is the distance between i and j on T. Constructing minimum ultrametric trees from distance matrices is an important problem in computational biology. In this paper, we examine its computational complexity and approximability. When the distances satisfy the triangle inequality, we show that the minimum ultrametric tree problem can be approximated in polynomial time with error ratio 1.5(1 + ⌈log n⌉), where n is the number of species. We also develop an efficient branch-and-bound algorithm for constructing the minimum ultrametric tree for both metric and non-metric inputs. The experimental results show that it can find an optimal solution for 25 species within reasonable time, while, to the best of our knowledge, there is no report of algorithms solving the problem even for 12 species.