Related papers: A tropical interpretation of m-dissimilarity maps

Let T be a weighted tree with n leaves. Let D_{i,j} be the distance between the leaves i and j. Let D_{i,j,k}= (D_{i,j} + D_{j,k} +D_{i,k})/2. We will call such numbers "triple weights" of the tree. In this paper, we give a…

In this article, we will prove that the set of 4-dissimilarity vectors of n-trees is contained in the tropical Grassmannian G_{4,n}. We will also propose three equivalent conjectures related to the set of m-dissimilarity vectors of n-trees…

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…

Let T be a (not necessarily positive) weighted tree with n leaves numbered by the set {1,...,n}. Define the k-weights of the tree D_{i_1,....,i_k}(T) as the sum of the lengths of the edges of the minimal subtree connecting i_1,....,i_k. We…

Let $p',q'\in R^n$. Write $p'\sim q'$ if $p'-q'$ is a multiple of $(1,\ldots,1)$. Two different points $p$ and $q$ in $R^n/\sim$ uniquely determine a tropical line $L(p,q)$, passing through them, and stable under small perturbations. This…

We give another proof that $m$-dissimilarity vectors of weighted trees are points on the tropical Grassmanian, as conjectured by Cools, and proved by Giraldo in response to a question of Sturmfels and Pachter. We accomplish this by relating…

Let ${\cal T}=(T,w)$ be a weighted finite tree with leaves $1,..., n$.For any $I :=\{i_1,..., i_k \} \subset \{1,...,n\}$, let $D_I ({\cal T})$ be the weight of the minimal subtree of $T$ connecting $i_1,..., i_k$; the $D_{I} ({\cal T})$…

The \emph{distance matrix} of a simple connected graph $G$ is $D(G)=(d_{ij})$, where $d_{ij}$ is the distance between the vertices $i$ and $j$ in $G$. We consider a weighted tree $T$ on $n$ vertices with edge weights are square matrix of…

In this short writing we prove that the set of m-dissimilarity vectors of n-trees is contained in the (m,n)-tropical Grassmannian, answering a question of Pachter and Speyer. We do this by proving a generalization of an equivalent…

Let $T$ be a tree with vertex set $\{1, \ldots, n\}$ such that each edge is assigned a nonzero weight. The squared distance matrix of $T,$ denoted by $\Delta,$ is the $n \times n$ matrix with $(i,j)$-element $d(i,j)^2,$ where $d(i,j)$ is…

Let $T$ be a tree on $n$ vertices whose edge weights are positive definite matrices of order $s$. The squared distance matrix of $T$, denoted by $\Delta$, is the $ns \times ns$ block matrix with $\Delta_{ij}=d(i,j)^2$, where $d(i,j)$ is the…

Let $n>1$ be an integer, and let $T$ be a tree with $n+1$ vertices $v_1,\ldots,v_{n+1}$, where $v_1$ and $v_{n+1}$ are two leaves of $T$. For each edge $e$ of $T$, assign a complex number $w(e)$ as its weight. We obtain that…

We revisit the representation theory in type $A$used previously to establish that the dissimilarity vectors of phylogenetic trees are points on the tropical Grassmannian variety. We use a different version of this construction to show that…

Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…

A k-dissimilarity D on a finite set X, |X| >= k, is a map from the set of size k subsets of X to the real numbers. Such maps naturally arise from edge-weighted trees T with leaf-set X: Given a subset Y of X of size k, D(Y) is defined to be…

Let ${\cal T}=(T,w)$ be a weighted finite tree with leaves $1,..., n$. For any $I :=\{i_1,..., i_k \} \subset \{1,...,n\}$, let $D_I ({\cal T})$ be the weight of the minimal subtree of $T$ connecting $i_1,..., i_k$; the $D_{I} ({\cal T})$…

Let ${\cal T}=(T,w)$ be a positive-weighted tree with at least $n$ vertices. For any $i,j \in \{1,...,n\}$, let $D_{i,j} ({\cal T})$ be the weight of the unique path in $T$ connecting $i$ and $j$. The $D_{i,j} ({\cal T})$ are called…

We propose a new topological invariant of unlabeled trees of N nodes. The invariant is a set of Nx2 matrices of integers, with sum_j k^{d_{i,j}} and v_i as the matrix elements, where d_{i,j} are the elements of the distance matrix and v_i…

It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…

In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…