Related papers: Classifying Tree Topologies along Tropical Line Se…
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 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…
Phylogenetic networks are rooted, labelled directed acyclic graphs which are commonly used to represent reticulate evolution. There is a close relationship between phylogenetic networks and multi-labelled trees (MUL-trees). Indeed, any…
We present a simple and elementary procedure to sketch the tropical conic given by a degree--two homogeneous tropical polynomial. These conics are trees of a very particular kind. Given such a tree, we explain how to compute a defining…
We prove that any graph $G$ with $n$ points has a distribution $\mathcal{T}$ over spanning trees such that for any edge $(u,v)$ the expected stretch $E_{T \sim \mathcal{T}}[d_T(u,v)/d_G(u,v)]$ is bounded by $\tilde{O}(\log n)$. Our result…
We show that the transience or recurrence of a random walk in certain random environments on an arbitrary infinite locally finite tree is determined by the branching number of the tree, which is a measure of the average number of branches…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
In biology, a phylogenetic tree is a tool to represent the evolutionary relationship between species. Unfortunately, the classical Schr\"oder tree model is not adapted to take into account the chronology between the branching nodes. In…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
We define the tropical moduli space of covers of a tropical line in the plane as weighted abstract polyhedral complex, and the tropical branch map recording the images of the simple ramifications. Our main result is the invariance of the…
The operation of transforming one spanning tree into another by replacing an edge has been considered widely, both for general and planar straight-line graphs. For the latter, several variants have been studied (e.g., edge slides and edge…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Let $G$ be a graph and $T_1,T_2$ be two spanning trees of $G$. We say that $T_1$ can be transformed into $T_2$ via an edge flip if there exist two edges $e \in T_1$ and $f$ in $T_2$ such that $T_2= (T_1 \setminus e) \cup f$. Since spanning…
In this paper we use the connections between tropical algebraic geometry and rigid analytic geometry in order to prove two main results. We use tropical methods to prove a theorem about the Newton polygon for convergent power series in…
A permutation $\boldsymbol w$ gives rise to a graph $G_{\boldsymbol w}$; the vertices of $G_{\boldsymbol w}$ are the letters in the permutation and the edges of $G_{\boldsymbol w}$ are the inversions of $\boldsymbol w$. We find that the…
Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and…
We give several characterizations of stable intersections of tropical cycles and establish their fundamental properties. We prove that the stable intersection of two tropical varieties is the tropicalization of the intersection of the…
The purpose of these notes is to clarify the duality between a natural class of jump processes on compact ultrametric spaces - studied in current work of Bendikov, Girgor'yan and Pittet - and nearest neighbour walks on trees. Processes of…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…