Related papers: From unicellular fatgraphs to trees
In this paper we present a topological framework for studying signed permutations and their reversal distance. As a result we can give an alternative approach and interpretation of the Hannenhalli-Pevzner formula for the reversal distance…
Felsner introduced a cycle reversal, namely the `flip' reversal, for \alpha-orientations (i.e., each vertex admits a prescribed out-degree) of a graph G embedded on the plane and further proved that the set of all the \alpha-orientations of…
Given a graph drawn in the plane, the degenerate crossing number of the drawing is the number of points in the plane which are contained in the relative interior of at least two edges, where each edge is required to be drawn as a simple…
The tree-metric theorem provides a necessary and sufficient condition for a dissimilarity matrix to be a tree metric, and has served as the foundation for numerous distance-based reconstruction methods in phylogenetics. Our main result is…
We introduce a new model of proteins, which extends and enhances the traditional graphical representation by associating a combinatorial object called a fatgraph to any protein based upon its intrinsic geometry. Fatgraphs can easily be…
In this paper we study planar morphs between straight-line planar grid drawings of trees. A morph consists of a sequence of morphing steps, where in a morphing step vertices move along straight-line trajectories at constant speed. We show…
If a graph has a non-singular adjacency matrix, then one may use the inverse matrix to define a (labeled) graph that may be considered to be the inverse graph to the original one. It has been known that an adjacency matrix of a tree is…
We consider unicellular maps, or polygon gluings, of fixed genus. A few years ago the first author gave a recursive bijection transforming unicellular maps into trees, explaining the presence of Catalan numbers in counting formulas for…
A method for considering a weighted directed graph with an accuracy of up to a given partition of the set of vertices is proposed. The resulting digraph (the splitting graph) does not contain arcs inside each partition element, and the arcs…
It is a classical result that any finite tree with positively weighted edges, and without vertices of degree 2, is uniquely determined by the weighted path distance between each pair of leaves. Moreover, it is possible for a (small) strict…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…
The self-similar structure of the attracting subshift of a primitive substitution is carried over to the limit set of the repelling tree in the boundary of Outer Space of the corresponding irreducible outer automorphism of a free group.…
In this work, we study methodical decomposition of an undirected, unweighted complete graph ($K_n$ of order $n$, size $m$) into minimum number of edge-disjoint trees. We find that $x$, a positive integer, is minimum and…
A unicellular map, or one-face map, is a graph embedded in an orientable surface such that its complement is a topological disk. In this paper, we give a new viewpoint to the structure of these objects, by describing a decomposition of any…
We consider spanning trees of $n$ points in convex position whose edges are pairwise non-crossing. Applying a flip to such a tree consists in adding an edge and removing another so that the result is still a non-crossing spanning tree.…
Tanglegrams are drawings of two rooted binary phylogenetic trees and a matching between their leaf sets. The trees are drawn crossing-free on opposite sides with their leaf sets facing each other on two vertical lines. Instead of minimizing…
A triangle decomposition of a graph is a partition of its edges into triangles. A fractional triangle decomposition of a graph is an assignment of a non-negative weight to each of its triangles such that the sum of the weights of the…
The analysis of objects living on ultrametric trees, in particular the block-diagonalization of 4-replica matrices $M^{\alpha \beta ; \gamma \delta}$, is shown to be dramatically simplified through the introduction of properly chosen…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Rooted phylogenetic networks are often constructed by combining trees, clusters, triplets or characters into a single network that in some well-defined sense simultaneously represents them all. We review these four models and investigate…