The distory package provides functions for computing geodesic distances between phylogenetic trees, as well as functions which use this distance. Methods for computing Gromov delta-hyperbolicity, Markov Chain Monte Carlo routines in tree space, and per-position leverage for DNA sequences are included.
A description of the algorithm used for the distance computation can
be found in dist.multiPhylo.
Chakerian, J. and Holmes, S. P. Computational Tools for Evaluating Phylogenetic and Heirarchical Clustering Trees. arXiv:1006.1015v1.
Billera, L. J., Holmes, S. P., and Vogtmann, K. (2001) Geometry of the space of phylogenetic trees. Advances in Applied Mathematics, 27, 733_-767.
Megan Owen and J. Scott Provan (2010) A fast algorithm for computing geodesic distances in tree space. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 14 Jan. 2010.