GitHub
The latest versions of the source code and jar files are available on GitHub at https://github.com/megan-owen/BHVtreespace
TreeStats software (IPMI 2013 paper)
Code for doing approximate Principal Components Analysis, mean and variance hypothesis testing, and Linear Discriminant Analysis (LDA)in tree space. (Matlab, Java, and Python).
Download: here (Java source code available upon request)
To cite, please reference: A. Feragen, M. Owen, J. Petersen, M.M.W. Wille, L.H. Thomsen, A. Dirksen, M. de Bruijne. Tree-space statistics and approximations for large-scale analysis of anatomical trees, Proceedings of 23rd biennial International Conference on Information Processing in Medical Imaging (IPMI), pp. 74-85, 2013.
SturmMean
Computes the Frechet mean and variance of phylogenetic trees (Java implementation).
Download: here (includes source code)
To cite, please reference: E. Miller, M. Owen and J.S. Provan. Polyhedral computational geoemtry for averaging metric phylogenetic trees, Advances in Applied Mathematics 68:51-91, 2015.
GTP
Computes the geodesic distance between phylogenetic trees in polynomial time (Java implementation).
Download: here (includes source code)
To cite, please reference: M. Owen and J.S. Provan. A fast algorithm for computing geodesic distances in tree space. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8:2-13, 2011.
GeodeMaps
Computes the geodesic distance between phylogenetic trees in exponential time (Java implementation).
Download: here (includes source code)
To cite, please reference: M. Owen. Computing geodesic distances in tree space. SIAM Journal on Discrete Mathematics, 25:1506-1529, 2011.