Related papers: On Two Measures of Distance between Fully-Labelled…

Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

A multilabeled tree (or MUL-tree) is a rooted tree in which every leaf is labelled by an element from some set, but in which more than one leaf may be labelled by the same element of that set. In phylogenetics, such trees are used in…

In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…

Edit distances between merge trees of scalar fields have many applications in scientific visualization, such as ensemble analysis, feature tracking or symmetry detection. In this paper, we propose branch mappings, a novel approach to the…

In this paper, we consider the Uniform Cost-Distance Steiner Tree Problem in metric spaces, a generalization of the well-known Steiner tree problem. Cost-distance Steiner trees minimize the sum of the total length and the weighted path…

Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…

CONTEXT. Attack treesare a recommended threat modeling tool, but there is no established method to compare them. OBJECTIVE. We aim to establish a method to compare "real" attack trees, based on both the structure of the tree itself and the…

Labelled Markov chains (LMCs) are widely used in probabilistic verification, speech recognition, computational biology, and many other fields. Checking two LMCs for equivalence is a classical problem subject to extensive studies, while the…

The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an algorithm that is explicitly polynomial time…

Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…

We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…

A rearrangement operation makes a small graph-theoretical change to a phylogenetic network to transform it into another one. For unrooted phylogenetic trees and networks, popular rearrangement operations are tree bisection and reconnection…

Tree rearrangement operations typically induce a metric on the space of phylogenetic trees. One important property of these metrics is the size of the neighbourhood, that is, the number of trees exactly one operation from a given tree. We…

Compression and sparsification algorithms are frequently applied in a preprocessing step before analyzing or optimizing large networks/graphs. In this paper we propose and study a new framework contracting edges of a graph (merging vertices…

We present new and improved fixed-parameter algorithms for computing maximum agreement forests (MAFs) of pairs of rooted binary phylogenetic trees. The size of such a forest for two trees corresponds to their subtree prune-and-regraft…

Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…

Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…

Given two messages - as linear sequences of letters, it is immediate to determine whether one can be transformed into the other by simple substitution cipher of the letters. On the other hand, if the letters are carried as labels on nodes…

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling…