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 arises in areas such as phylogenetics, linguistics, etc. e.g., 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 [MS05], 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 strings.

In this paper we continue the work of [MS05], 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 2) 3-approximation algorithm for convex recoloring of trees.


Covered Vertex Partial Coloring Colored Tree Perfect Phylogeny Versus Support 
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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Shlomo Moran
    • 1
  • Sagi Snir
    • 2
  1. 1.Computer Science deptTechnionHaifaIsrael
  2. 2.Mathematics deptUniversity of CaliforniaBerkeleyUSA

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