Efficient Approximation of Convex Recolorings

A coloring of a tree is convex if the vertices that pertain to any color induce a connected subtree; a partial coloring (which assigns colors to some of the vertices) is convex if it can be completed to a convex (total) coloring. Convex coloring of trees arise in areas such as phylogenetics, linguistics, etc. eg, a perfect phylogenetic tree is one in which the states of each character induce a convex coloring of the tree. Research on perfect phylogeny is usually focused on finding a tree so that few predetermined partial colorings of its vertices are convex. When a coloring of a tree is not convex, it is desirable to know ”how far” it is from a convex one. In [19], a natural measure for this distance, called the recoloring distance was defined: the minimal number of color changes at the vertices needed to make the coloring convex. This can be viewed as minimizing the number of “exceptional vertices” w.r.t. to a closest convex coloring. The problem was proved to be NP-hard even for colored string. In this paper we continue the work of [19], and present a 2-approximation algorithm of convex recoloring of strings whose running time O(cn), where c is the number of colors and n is the size of the input, and an O(cn)-time 3-approximation algorithm for convex recoloring of trees. A preliminary version of the results in this paper appeared in [18]. Computer Science dept., Technion, Haifa 32000, Israel. [email protected] Department of Mathematics, University of California, Berkeley, CA 94720, USA [email protected]