Related papers: Reconstruction of caterpillar tanglegrams
Topologically constrained genome-like polymers often double-fold into tree-like configurations, which can be modelled on the level of folded (ring) polymers or on the level of the underlying random trees. For both descriptions, we have…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Tree trace reconstruction aims to learn the binary node labels of a tree, given independent samples of the tree passed through an appropriately defined deletion channel. In recent work, Davies, R\'acz, and Rashtchian used combinatorial…
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 present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
Phylogenetic networks are mathematical structures for modeling and visualization of reticulation processes in the study of evolution. Galled networks, reticulation visible networks, nearly-stable networks and stable-child networks are the…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
A tangram is a word in which every letter occurs an even number of times. Thus it can be cut into parts that can be arranged into two identical words. The \emph{cut number} of a tangram is the minimum number of required cuts in this…
By weighted tree we understand such connected tree,that: a) each its vertex and each edge have a positive integer weight; b) the weight of each vertex is equal to the sum of weights of outgoing edges. Each tree has a binary structure --- we…
A fringe subtree of a rooted tree is a subtree induced by one of the vertices and all its descendants. We consider the problem of estimating the number of distinct fringe subtrees in two types of random trees: simply generated trees and…
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level-$k$ networks. In a tree-child network, every non-leaf node has a child that is a tree…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Estimating phylogenetic trees, which depict the relationships between different species, from aligned sequence data (such as DNA, RNA, or proteins) is one of the main aims of evolutionary biology. However, tree reconstruction criteria like…
In a rooted tree, we call a vertex {\em balanced} if it is at equal distance from all its descendant leaves. We count balanced vertices in three different tree varieties. For decreasing binary trees, we can prove that the probability that a…
We prove a general width duality theorem for combinatorial structures with well-defined notions of cohesion and separation. These might be graphs and matroids, but can be much more general or quite different. The theorem asserts a duality…
A 2-tree is a graph that can be formed by starting with a triangle and iterating the operation of making a new vertex adjacent to two adjacent vertices of the existing graph. Leizhen Cai asked in 1995 whether every maximal planar graph…
A tree-based network $\mathcal N$ on $X$ is universal if every rooted binary phylogenetic $X$-tree is a base tree for $\mathcal N$. Hayamizu and, independently, Zhang constructively showed that, for all positive integers $n$, there exists…
Clustering is a well-known and studied problem, one of its variants, called contiguity-constrained clustering, accepts as a second input a graph used to encode prior information about cluster structure by means of contiguity constraints…
A $p$-caterpillar is a caterpillar such that every non-leaf vertex is adjacent to exactly $p$ leaves. We give a tight minimum degree condition for a graph to have a spanning $p$-caterpillar.