Related papers: On Determining if Tree-based Networks Contain Fixe…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
A directed phylogenetic network is tree-child if every non-leaf vertex has a child that is not a reticulation. As a class of directed phylogenetic networks, tree-child networks are very useful from a computational perspective. For example,…
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…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
One strategy for reconstruction of phylogenetic networks is to solve the phylogenetic network problem, which involves inferring phylogenetic trees first and subsequently computing the smallest phylogenetic network that displays all the…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
A rooted acyclic digraph N with labelled leaves displays a tree T when there exists a way to select a unique parent of each hybrid vertex resulting in the tree T. Let Tr(N) denote the set of all trees displayed by the network N. In general,…
Phylogenetic networks are a generalization of phylogenetic trees allowing for the representation of non-treelike evolutionary events such as hybridization. Typically, such networks have been analyzed based on their `level', i.e. based on…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
Algorithms for learning decision trees often include heuristic local-search operations such as (1) adjusting the threshold of a cut or (2) also exchanging the feature of that cut. We study minimizing the number of classification errors by…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Suppose N is a phylogenetic network indicating a complicated relationship among individuals and taxa. Often of interest is a much simpler network, for example, a species tree T, that summarizes the most fundamental relationships. The…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…
While every rooted binary phylogenetic tree is determined by its set of displayed rooted triples, such a result does not hold for an arbitrary rooted binary phylogenetic network. In particular, there exist two non-isomorphic rooted binary…