The Disk - Covering Method for Tree Reconstruction 631

Evolutionary tree reconstruction is a very important step in many biological research problems , and yet is extremely diicult for a variety of computational, statistical, and scientiic reasons. In particular, the reconstruction of very large trees containing signiicant amounts of divergence is especially challenging. We present in this paper a new tree reconstruction method, which we call the Disk-Covering Method, which can be used to recover accurate estimations of the evolutionary tree for otherwise intractable datasets. DCM obtains a decomposition of the input dataset into small overlapping sets of closely related taxa, reconstructs trees on these subsets (using a \base" phylogenetic method of choice), and then combines the subtrees into one tree on the entire set of taxa. Because the subproblems analyzed by DCM are smaller, com-putationally expensive methods such as maximum likelihood estimation can be used without incurring too much cost. At the same time, because the taxa within each subset are closely related, even very simple methods (such as neighbor-joining) are much more likely to be highly accurate. The result is that DCM-boosted methods are typically faster and more accurate as compared to \naive" use of the same method. In this paper we describe the basic ideas and techniques in DCM, and demonstrate the advantages of DCM experimentally by simulating sequence evolution on a variety of trees.