Related papers: Bounds for phylogenetic network space metrics
In mathematical phylogenetics, evolutionary relationships are often represented by trees and networks. The latter are typically used whenever the relationships cannot be adequately described by a tree, which happens when so-called…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…
Structural parameters of graphs, such as treewidth, play a central role in the study of the parameterized complexity of graph problems. Motivated by the study of parametrized algorithms on phylogenetic networks, scanwidth was introduced…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Phylogenetic networks are becoming increasingly popular in phylogenetics since they have the ability to describe a wider range of evolutionary events than their tree counterparts. In this paper, we study Markov models on phylogenetic…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
In the NP-hard Optimizing PD with Dependencies (PDD) problem, the input consists of a phylogenetic tree $T$ over a set of taxa $X$, a food-web that describes the prey-predator relationships in $X$, and integers $k$ and $D$. The task is to…
We study distorted metrics on binary trees in the context of phylogenetic reconstruction. Given a binary tree $T$ on $n$ leaves with a path metric $d$, consider the pairwise distances $\{d(u,v)\}$ between leaves. It is well known that these…
Phylogenomics is a new field which applies to tools in phylogenetics to genome data. Due to a new technology and increasing amount of data, we face new challenges to analyze them over a space of phylogenetic trees. Because a space of…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
We introduce a biologically natural, mathematically tractable model of random phylogenetic network to describe evolution in the presence of hybridization. One of the features of this model is that the hybridization rate of the lineages…
Normal networks are an important class of phylogenetic networks that have compelling mathematical properties which align with intuition about inference from genetic data. While tools enabling widespread use of phylogenetic networks in the…
A fundamental problem in network science is the normalization of the topological or physical distance between vertices, that requires understanding the range of variation of the unnormalized distances. Here we investigate the limits of the…
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…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…
In the Maximize Phylogenetic Diversity problem, we are given a phylogenetic tree that represents the genetic proximity of species, and we are asked to select a subset of species of maximum phylogenetic diversity to be preserved through…