The discrete Toda molecule equation can be used to compute eigenvalues of tridiagonal matrices over conventional linear algebra, and is the recursion formula of the well-known quotient difference algorithm for tridiagonal eigenvalues. An ultradiscretization of the discrete Toda equation leads to the ultradiscrete Toda (udToda) equation, which describes motions of balls in the box and ball system. In this paper, we associate the udToda equation with eigenvalues of tridiagonal matrices over min-plus algebra, which is a semiring with two operation types: and . We also clarify an interpretation of the udToda variables in weighted and directed graphs consisting of vertices and edges.