Related papers: Ranking top-k trees in tree-based phylogenetic net…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
A fundamental problem in the study of phylogenetic networks is to determine whether or not a given phylogenetic network contains a given phylogenetic tree. We develop a quadratic-time algorithm for this problem for binary nearly-stable…
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…
We propose a reinforcement-learning algorithm to tackle the challenge of reconstructing phylogenetic trees. The search for the tree that best describes the data is algorithmically challenging, thus all current algorithms for phylogeny…
Recently, so-called treebased phylogenetic networks have gained considerable interest in the literature, where a treebased network is a network that can be constructed from a phylogenetic tree, called the base tree, by adding additional…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
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 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 provide a more general description of evolutionary relationships than rooted phylogenetic trees. One way to produce a phylogenetic network is to randomly place $k$ arcs between the edges of a rooted binary phylogenetic…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and…
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…
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…
Random forests on the one hand, and neural networks on the other hand, have met great success in the machine learning community for their predictive performance. Combinations of both have been proposed in the literature, notably leading to…
In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…
Given a rooted, binary phylogenetic network and a rooted, binary phylogenetic tree, can the tree be embedded into the network? This problem, called \textsc{Tree Containment}, arises when validating networks constructed by phylogenetic…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…