A Fast Algorithm for Computing Geodesic Distances in Tree Space
2009年7月23日 · An important open problem is to find a polynomial time algorithm for finding geodesics in tree space, which starts with a simple initial path and moves through a series of successively shorter paths until the geodesic is attained. IEEE/ACM Transactions on Computational Biology…
Tom Nye’s site
the Owen-Provan algorithm for construction of geodesics in BHV tree space; projection of trees onto BHV geodesics; a variety of nucleotide and amino acid substitution models;
Phylogenetic Vignettes: Owen-Provan algorithm - Nicolae's …
2022年9月19日 · In this post we will provide a brief overview of the algorithm presented in Owen and Provan, 2010, which allows us to compute the geodesics in 𝛕 -space and BHV space in polynomial time (in the number of the tree leaves/taxa). For the ease of exposition we will delegate detailed overview of the BHV space to a later post.
Owen and Provan [23] proved that these geodesics can be computed in polynomial time. In Section 2, we present a detailed review and analysis. This is done in the setting of orthant spaces FΩ associated with flag simplicial complexes Ω. In Section 3 we study geodesically closed subsets of an orthant space FΩ, with primary focus on geodesic ...
[1510.08797] Convexity in Tree Spaces - arXiv.org
2015年10月29日 · While its geodesics can be computed by the Owen-Provan algorithm, geodesic triangles are complicated. We show that the dimension of such a triangle can be arbitrarily high. Tropical convexity and the tropical metric behave better. They exhibit properties desirable for geometric statistics, such as geodesics of small depth.
Scholars@Duke publication: Polyhedral computational geometry …
2015年7月1日 · Miller E, Owen M, Provan JS. Polyhedral computational geometry for averaging metric phylogenetic trees. Advances in Applied Mathematics. 2015 Jul 1;68:51–91.
Megan Owen - Teaching - Lehman
Polyhedral computational geoemtry for averaging metric phylogenetic trees, Advances in Applied Mathematics 68:51-91, 2015. Computes the geodesic distance between phylogenetic trees in polynomial time (Java implementation). To cite, please reference: M. Owen and J.S. Provan. A fast algorithm for computing geodesic distances in tree space.
Computing Geodesic Distances in Tree Space - Semantic Scholar
2009年3月3日 · The algorithm is a simple iterative method to update breakpoints of a path joining two points using Owen and Provan’s algorithm as a subroutine and is applicable to any path in any CAT (0) space in which geodesics between two close points can be computed.
Geometry Seminar -- April 26, 2016 -- Bernd Sturfels -- Abstract
2016年4月26日 · While its geodesics can be computed by the Owen-Provan algorithm, geodesic triangles are complicated and can have arbitrarily high dimension. Tropical convexity and the tropical metric are better behaved, as they exhibit properties that are desirable for geometric statistics. This is joint work with Bo Lin, Xioaxian Tang and Ruriko Yoshida.
GitHub - kgori/GTP: Megan Owen and Scott Provan's java …
A fork of Megan Owen and Scott Provan's java implementation of their GTP algorithm for calculating the geodesic distance between phylogenetic trees, from this paper. The original code only allowed for all-all comparisons, this version is modified to allow row-wise comparisons - i.e. the first tree in a file against all other trees.