Related papers: Quantifying the difference between phylogenetic di…
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…
Tree balance plays an important role in phylogenetics and other research areas, which is why several indices to measure tree balance have been introduced over the years. Nevertheless, a formal definition of what a balance index actually is…
For many graph-related problems, it can be essential to have a set of structurally diverse graphs. For instance, such graphs can be used for testing graph algorithms or their neural approximations. However, to the best of our knowledge, the…
Tree balance plays an important role in various research areas in phylogenetics and computer science. Typically, it is measured with the help of a balance index or imbalance index. There are more than 25 such indices available, recently…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Diversity is a central concept in many fields. Despite its importance, there is no unified methodological framework to measure diversity and its three components of variety, balance and disparity. Current approaches take into account…
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…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
We describe the use of the Frechet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Frechet mean is comparable to other summary methods,…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
In a deterministic or random tree, a notion of ancestral diversity can be defined as follows. Sample independently $n$ groups of $k$ leaves and count the number $N_n(k)$ of distinct most recent common ancestors of each of the groups. As $n$…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
In recent years, there has been an effort to extend the classical notion of phylogenetic balance, originally defined in the context of trees, to networks. One of the most natural ways to do this is with the so-called $B_2$ index. In this…
Whether or not biodiversity dynamics tend toward stable equilibria remains an unsolved question in ecology and evolution with important implications for our understanding of diversity and its conservation. Phylo/population genetic models…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…