Related papers: Split-facets for Balanced Minimal Evolution Polyto…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
Balanced minimum evolution (BME) is a statistically consistent distance-based method to reconstruct a phylogenetic tree from an alignment of molecular data. In 2000, Pauplin showed that the BME method is equivalent to optimizing a linear…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
The secondary polytope of a point configuration A is a polytope whose face poset is isomorphic to the poset of all regular subdivisions of A. While the vertices of the secondary polytope - corresponding to the triangulations of A - are very…
This paper investigates the problem of listing faces of combinatorial polytopes, such as hypercubes, permutahedra, associahedra, and their generalizations. Firstly, we consider the face lattice, which is the inclusion order of all faces of…
We define and study a new family of polytopes which are formed as convex hulls of partial alternating sign matrices. We determine the inequality descriptions, number of facets, and face lattices of these polytopes. We also study partial…
The $(m,n)$-multiplihedron is a polytope whose faces correspond to $m$-painted $n$-trees, and whose oriented skeleton is the Hasse diagram of the rotation lattice on binary $m$-painted $n$-trees. Deleting certain inequalities from the facet…
We exhibit several posets arising from commutative algebra, order theory, tropical convexity as potential face posets of tropical polyhedra, and we clarify their inclusion relations. We focus on monomial tropical polyhedra, and deduce how…
We investigate a poset structure that extends the weak order on a finite Coxeter group $W$ to the set of all faces of the permutahedron of $W$. We call this order the facial weak order. We first provide two alternative characterizations of…
Faces play a central role in the combinatorial and computational aspects of polyhedra. In this paper, we present the first formalization of faces of polyhedra in the proof assistant Coq. This builds on the formalization of a library…
This paper initiates the explicit study of face numbers of matroid polytopes and their computation. We prove that, for the large class of split matroid polytopes, their face numbers depend solely on the number of cyclic flats of each rank…
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…
The Total Matching Polytope generalizes the Stable Set Polytope and the Matching Polytope. In this paper, we give the perfect formulation for Trees and we derive two new families of valid inequalities, the balanced biclique inequalities…
We consider facet-Hamiltonian cycles of polytopes, defined as cycles in their skeleton such that every facet is visited exactly once. These cycles can be understood as optimal watchman routes that guard the facets of a polytope. We consider…
We study nested complexes of building sets on the Las Vergnas face lattices of oriented matroids. Such a nested complex is the face lattice of an oriented matroid, obtained by iterated stellar subdivisions of the positive tope. If the…
The classical permutohedron Perm is the convex hull of the points (w(1),...,w(n)) in R^n where w ranges over all permutations in the symmetric group. This polytope has many beautiful properties -- for example it provides a way to visualize…
A permutation polytope is the convex hull of a group of permutation matrices. In this paper we investigate the combinatorics of permutation polytopes and their faces. As applications we completely classify permutation polytopes in…
Motivated by the work of Panina and her coauthors on cyclopermutohedron we study a poset whose elements correspond to equivalence classes of partitions of the set $\{1,\cdots, n+1\}$ up to cyclic permutations and orientation reversion. This…
In this paper we present an explicit combinatorial description of a special class of facets of the secondary polytopes of hypersimplices. These facets correspond to polytopal subdivisions called multi-splits. We show a relation between the…