4,541 research outputs found

    Toric ideals of homogeneous phylogenetic models

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    We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric ideal of invariants for trees with up to 11 nodes. These are perhaps the first non-trivial Grobner bases calculations in 2^11 indeterminates. We conjecture that there is a quadratic Grobner basis for binary trees. Finally, we give a explicit description of the polytope associated to this toric ideal for an infinite family of binary trees and conjecture that there is a universal bound on the number of vertices of this polytope for binary trees.Comment: 6 pages, 17 figure

    A Polyhedral Intersection Theorem for Capacitated Spanning Trees

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    In a two-capacitated spanning tree of a complete graph with a distinguished root vertex v, every component of the induced subgraph on V\{v} has at most two vertices. We give a complete,non-redundant characterization of the polytope defined by the convex hull of the incidence vectors of two-capacitated spanning trees. This polytope is the intersection of the spanning tree polytope on the given graph and the matching polytope on the subgraph induced by removing the root node and its incident edges. This result is one of very few known cases in which the intersection of two integer polyhedra yields another integer polyhedron. We also give a complete polyhedral characterization of a related polytope, the 2-capacitated forest polytope

    Polyhedral geometry of Phylogenetic Rogue Taxa

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    It is well known among phylogeneticists that adding an extra taxon (e.g. species) to a data set can alter the structure of the optimal phylogenetic tree in surprising ways. However, little is known about this "rogue taxon" effect. In this paper we characterize the behavior of balanced minimum evolution (BME) phylogenetics on data sets of this type using tools from polyhedral geometry. First we show that for any distance matrix there exist distances to a "rogue taxon" such that the BME-optimal tree for the data set with the new taxon does not contain any nontrivial splits (bipartitions) of the optimal tree for the original data. Second, we prove a theorem which restricts the topology of BME-optimal trees for data sets of this type, thus showing that a rogue taxon cannot have an arbitrary effect on the optimal tree. Third, we construct polyhedral cones computationally which give complete answers for BME rogue taxon behavior when our original data fits a tree on four, five, and six taxa. We use these cones to derive sufficient conditions for rogue taxon behavior for four taxa, and to understand the frequency of the rogue taxon effect via simulation.Comment: In this version, we add quartet distances and fix Table 4

    Enumerating Foldings and Unfoldings between Polygons and Polytopes

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    We pose and answer several questions concerning the number of ways to fold a polygon to a polytope, and how many polytopes can be obtained from one polygon; and the analogous questions for unfolding polytopes to polygons. Our answers are, roughly: exponentially many, or nondenumerably infinite.Comment: 12 pages; 10 figures; 10 references. Revision of version in Proceedings of the Japan Conference on Discrete and Computational Geometry, Tokyo, Nov. 2000, pp. 9-12. See also cs.CG/000701

    Examples, Counterexamples, and Enumeration Results for Foldings and Unfoldings between Polygons and Polytopes

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    We investigate how to make the surface of a convex polyhedron (a polytope) by folding up a polygon and gluing its perimeter shut, and the reverse process of cutting open a polytope and unfolding it to a polygon. We explore basic enumeration questions in both directions: Given a polygon, how many foldings are there? Given a polytope, how many unfoldings are there to simple polygons? Throughout we give special attention to convex polygons, and to regular polygons. We show that every convex polygon folds to an infinite number of distinct polytopes, but that their number of combinatorially distinct gluings is polynomial. There are, however, simple polygons with an exponential number of distinct gluings. In the reverse direction, we show that there are polytopes with an exponential number of distinct cuttings that lead to simple unfoldings. We establish necessary conditions for a polytope to have convex unfoldings, implying, for example, that among the Platonic solids, only the tetrahedron has a convex unfolding. We provide an inventory of the polytopes that may unfold to regular polygons, showing that, for n>6, there is essentially only one class of such polytopes.Comment: 54 pages, 33 figure

    On the optimality of the neighbor-joining algorithm

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    The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a dissimilarity map. From this point of view, NJ is ``optimal'' when the algorithm outputs the tree which minimizes the balanced minimum evolution criterion. We use the fact that the NJ tree topology and the BME tree topology are determined by polyhedral subdivisions of the spaces of dissimilarity maps R+(n2){\R}_{+}^{n \choose 2} to study the optimality of the neighbor-joining algorithm. In particular, we investigate and compare the polyhedral subdivisions for n≤8n \leq 8. A key requirement is the measurement of volumes of spherical polytopes in high dimension, which we obtain using a combination of Monte Carlo methods and polyhedral algorithms. We show that highly unrelated trees can be co-optimal in BME reconstruction, and that NJ regions are not convex. We obtain the l2l_2 radius for neighbor-joining for n=5n=5 and we conjecture that the ability of the neighbor-joining algorithm to recover the BME tree depends on the diameter of the BME tree
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