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Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…
We first show that increasing trees are in bijection with set compositions, extending simultaneously a recent result on trees due to Tonks and a classical result on increasing binary trees. We then consider algebraic structures on the…
We develop the Tree-Loop Duality Relation for two- and three-loop integrals with multiple identical propagators (multiple poles). This is the extension of the Duality Relation for single poles and multiloop integrals derived in previous…
Let T1, T2,.... Tk be spanning trees in a graph G. If for any pair of vertices u and v of G, the paths between u and v in every Ti( 0 < i < k+1) do not contain common edges then T1, T2,.... Tk are called edge-disjoint spanning trees in G.…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
A permutation graph is a graph whose edges are given by inversions of a permutation. We study the Abelian sandpile model (ASM) on such graphs. We exhibit a bijection between recurrent configurations of the ASM on permutation graphs and the…
Tanglegrams are formed by taking two rooted binary trees $T$ and $S$ with the same number of leaves and uniquely matching each leaf in $T$ with a leaf in $S$. They are usually represented using layouts, which embed the trees and the…
The duality relation between one-loop integrals and phase-space integrals, developed in a previous work, is extended to higher-order loops. The duality relation is realized by a modification of the customary +i0 prescription of the Feynman…
Efforts to reconstruct phylogenetic trees and understand evolutionary processes depend fundamentally on stochastic models of speciation and mutation. The simplest continuous-time model for speciation in phylogenetic trees is the Yule…
Crossover and mutation are the two main operators that lead to new solutions in evolutionary approaches. In this article, a new method of performing the crossover phase is presented. The problem of choice is evolutionary decision tree…
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…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Permutation polynomials over finite fields constitute an active research area and have applications in many areas of science and engineering. In this paper, two conjectures on permutation polynomials proposed recently by Wu and Li [19] are…
The reconstruction of transmission trees for epidemics from genetic data has been the subject of some recent interest. It has been demonstrated that the transmission tree structure can be investigated by augmenting internal nodes of a…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…
Partial duality is a duality of ribbon graphs relative to a subset of their edges generalizing the classical Euler-Poincare duality. This operation often changes the genus. Recently J.L.Gross, T.Mansour, and T.W.Tucker formulated a…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…
In this paper we consider two continuous-mass population models as analogues of logistic branching random walks, one is supported on a finite trait space and the other one is supported on an infinite trait space. For the first model with…
We propose several constructions of commutative or cocommutative Hopf algebras based on various combinatorial structures, and investigate the relations between them. A commutative Hopf algebra of permutations is obtained by a general…