Related papers: Visualizing Co-Phylogenetic Reconciliations
When solving ill-posed inverse problems, one often desires to explore the space of potential solutions rather than be presented with a single plausible reconstruction. Valuable insights into these feasible solutions and their associated…
Multi-faceted data visualization typically involves several dedicated views. To create a comprehensive understanding of the data, users have to mentally integrate the information from the different views. This integration is hindered by…
Merge trees are a type of topological descriptors that record the connectivity among the sublevel sets of scalar fields. They are among the most widely used topological tools in visualization. In this paper, we are interested in sketching a…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Generalized Pythagoras trees were developed for visualizing hierarchical data, producing organic, fractal-like representations. However, the drawback of the original layout algorithm is visual overlap of tree branches. To avoid such…
Storyline visualizations help visualize encounters of the characters in a story over time. Each character is represented by an x-monotone curve that goes from left to right. A meeting is represented by having the characters that participate…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
We develop a new method for visualizing and refining the invariances of learned representations. Specifically, we test for a general form of invariance, linearization, in which the action of a transformation is confined to a low-dimensional…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
The visualization of hierarchically structured data over time is an ongoing challenge and several approaches exist trying to solve it. Techniques such as animated or juxtaposed tree visualizations are not capable of providing a good…
Throughout the last decade, we have seen much progress towards characterising and computing the minimum hybridisation number for a set P of rooted phylogenetic trees. Roughly speaking, this minimum quantifies the number of hybridisation…
Storyline visualizations show the structure of a story, by depicting the interactions of the characters over time. Each character is represented by an x-monotone curve from left to right, and a meeting is represented by having the curves of…
We present an algorithmic technique for visualizing the co-authorship networks and other networks modeled with hypergraphs (set systems). As more than two researchers can co-author a paper, a direct representation of the interaction of…
Existing genetic programming (GP) methods are typically designed based on a certain representation, such as tree-based or linear representations. These representations show various pros and cons in different domains. However, due to the…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…
Recent work has proven the existence of extreme inbreeding in a European ancestry sample taken from the contemporary UK population \cite{nature_01}. This result brings our attention again to a math problem related to inbreeding family trees…