Related papers: Most Compact Parsimonious Trees
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
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.…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
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…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
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 generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…
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.…