Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths is the length of the shortest path between them in the continuous tree space introduced by Billera, Holmes, and Vogtmann. This tree space provides a powerful tool for studying and comparing phylogenetic trees, both in exhibiting a natural distance measure and in providing a Euclideanlike structure for solving optimization problems on trees. An important open problem is to find a polynomial time algorithm for finding geodesics in tree space. This paper gives such an algorithm, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained.

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We describe an algorithm to compute the geodesics in an arbitrary CAT(0) cubical complex. A key tool is a correspondence between cubical complexes of global non-positive curvature and posets with inconsistent pairs. This correspondence also gives an explicit realization of such a complex as the state complex of a reconfigurable system, and a way to embed any interval in the integer lattice cubing of its dimension.

Given a probability distribution on an open book (a metric space obtained by gluing a disjoint union of copies of a half-space along their boundary hyperplanes), we define a precise concept of when the Fr\'{e}chet mean (barycenter) is sticky. This nonclassical phenomenon is quantified by a law of large numbers (LLN) stating that the empirical mean eventually almost surely lies on the (codimension $1$ and hence measure $0$) spine that is the glued hyperplane, and a central limit theorem (CLT) stating that the limiting distribution is Gaussian and supported on the spine. We also state versions of the LLN and CLT for the cases where the mean is nonsticky (i.e., not lying on the spine) and partly sticky (i.e., is, on the spine but not sticky).Comment: Published in at http://dx.doi.org/10.1214/12-AAP899 the Annals of Applied Probability (http://www.imstat.org/aap/) by the Institute of Mathematical Statistics (http://www.imstat.org

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