Related papers: Reconstructing fully-resolved trees from triplet c…
We study multicolour, oriented and high-dimensional discrepancies of the set of all subtrees of a tree. As our main result, we show that the $r$-colour discrepancy of the subtrees of any tree is a linear function of the number of leaves…
An important problem in geometric computing is defining and computing similarity between two geometric shapes, e.g. point sets, curves and surfaces, etc. Important geometric and topological information of many shapes can be captured by…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
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…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Harary and Lauri conjectured that the class reconstruction number of trees is 2, that is, each tree has two unlabelled vertex-deleted subtrees that are not both in the deck of any other tree. We show that each tree $T$ can be reconstructed…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
We consider a procedure to reduce simply generated trees by iteratively removing all leaves. In the context of this reduction, we study the number of vertices that are deleted after applying this procedure a fixed number of times by using…
We prove that every positively-weighted tree T can be realized as the cut locus C(x) of a point x on a convex polyhedron P, with T weights matching C(x) lengths. If T has n leaves, P has (in general) n+1 vertices. We show there are in fact…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…
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…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
The reconstruction of a central tendency `species tree' from a large number of conflicting gene trees is a central problem in systematic biology. Moreover, it becomes particularly problematic when taxon coverage is patchy, so that not all…
There are many fundamental algorithmic problems on triangulated 3-manifolds whose complexities are unknown. Here we study the problem of finding a taut angle structure on a 3-manifold triangulation, whose existence has implications for both…
The $(n-\ell)$-deck of an $n$-vertex graph is the multiset of (unlabeled) subgraphs obtained from it by deleting $\ell$ vertices. An $n$-vertex graph is $\ell$-reconstructible if it is determined by its $(n-\ell)$-deck, meaning that no…
Leaves, i.e., vertices of degree one, can play a significant role in graph structure, especially in sparsely connected settings in which leaves often constitute the largest fraction of vertices. We consider a leaf-based counterpart of the…
We tackle the challenging problem of creating full and accurate three dimensional reconstructions of botanical trees with the topological and geometric accuracy required for subsequent physical simulation, e.g. in response to wind forces.…
Tree containment problem is a fundamental problem in phylogenetic study, as it is used to verify a network model. It asks whether a given network contain a subtree that resembles a binary tree. The problem is NP-complete in general, even in…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…