Code



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.





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