Related papers: Locating a Tree in a Reticulation-Visible Network …
Semidirected networks have received interest in evolutionary biology as the appropriate generalization of unrooted trees to networks, in which some but not all edges are directed. Yet these networks lack proper theoretical study. We define…
Recently, there has been a growing interest in the relationships between unrooted and rooted phylogenetic networks. In this context, a natural question to ask is if an unrooted phylogenetic network U can be oriented as a rooted phylogenetic…
In evolutionary biology, phylogenetic networks are graphs that provide a flexible framework for representing complex evolutionary histories that involve reticulate evolutionary events. Recently phylogenetic studies have started to focus on…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Semi-labeled trees are phylogenies whose internal nodes may be labeled by higher-order taxa. Thus, a leaf labeled Mus musculus could nest within a subtree whose root node is labeled Rodentia, which itself could nest within a subtree whose…
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.…
Phylogenetic networks are rooted directed acyclic graphs that represent evolutionary relationships between species whose past includes reticulation events such as hybridisation and horizontal gene transfer. To search the space of…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
Given a finite set $X$, a collection $\mathcal{T}$ of rooted phylogenetic trees on $X$ and an integer $k$, the Hybridization Number problem asks if there exists a phylogenetic network on $X$ that displays all trees from $\mathcal{T}$ and…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
A graph is a $k$-leaf power of a tree $T$ if its vertices are leaves of $T$ and two vertices are adjacent in $T$ if and only if their distance in $T$ is at most $k$. Then $T$ is a $k$-leaf root of $G$. This notion was introduced by…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
We present a complete classification of the deterministic distributed time complexity for a family of graph problems: binary labeling problems in trees. These are locally checkable problems that can be encoded with an alphabet of size two…
We investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
A challenging problem in complex networks is the network reconstruction problem from data. This work deals with a class of networks denoted as conserved networks, in which a flow associated with every edge and the flows are conserved at all…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
It is a known fact that, given two rooted binary phylogenetic trees, the concept of maximum acyclic agreement forests is sufficient to compute hybridization networks with minimum hybridization number. In this work, we demonstrate by first…