There are several common ways to encode a tree as a matrix, such as the
adjacency matrix, the Laplacian matrix (that is, the infinitesimal generator of
the natural random walk), and the matrix of pairwise distances between leaves.
Such representations involve a specific labeling of the vertices or at least
the leaves, and so it is natural to attempt to identify trees by some feature
of the associated matrices that is invariant under relabeling. An obvious
candidate is the spectrum of eigenvalues (or, equivalently, the characteristic
polynomial). We show for any of these choices of matrix that the fraction of
binary trees with a unique spectrum goes to zero as the number of leaves goes
to infinity. We investigate the rate of convergence of the above fraction to
zero using numerical methods. For the adjacency and Laplacian matrices, we show
that that the {\em a priori} more informative immanantal polynomials have no
greater power to distinguish between trees