Related papers: Locating a Phylogenetic Tree in a Reticulation-Vis…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent reticulate evolution. Unrooted phylogenetic networks form a special class of such networks, which naturally generalize unrooted phylogenetic trees.…
'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…
Phylogenetic networks are used to represent the evolutionary history of species. They are versatile when compared to traditional phylogenetic trees, as they capture more complex evolutionary events such as hybridization and horizontal gene…
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…
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
The inference of the evolutionary history of a collection of organisms is a problem of fundamental importance in evolutionary biology. The abundance of DNA sequence data arising from genome sequencing projects has led to significant…
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…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
Rooted binary phylogenetic networks are extensions of rooted binary trees, adding reticulation nodes that are designed to represent evolutionary processes that involve hybridization events. Enumerative combinatorics studies have counted…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
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…
Phylogenetic networks generalize evolutionary trees, and are commonly used to represent evolutionary histories of species that undergo reticulate evolutionary processes such as hybridization, recombination and lateral gene transfer.…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
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…
Galled trees are widely studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into galled networks by relaxing a structural condition. In this work, a linear recurrence formula is given…
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…
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…
Tree-child networks are one of the most prominent network classes for modeling evolutionary processes which contain reticulation events. Several recent studies have addressed counting questions for {\it bicombining tree-child networks}…
Reticulate evolution gives rise to complex phylogenetic networks, making their interpretation challenging. A typical approach is to extract trees within such networks. Since Francis and Steel's seminal paper, "Which Phylogenetic Networks…
We study the problem of finding a temporal hybridization network for a set of phylogenetic trees that minimizes the number of reticulations. First, we introduce an FPT algorithm for this problem on an arbitrary set of $m$ binary trees with…