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Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Phylogenetic networks provide a framework for representing evolutionary histories involving reticulate events such as hybridization or horizontal gene transfer. A central problem is to infer such networks from local structural information.…
Phylogenetic networks are an extension of phylogenetic trees that allow for the representation of reticulate evolution events. One of the classes of networks that has gained the attention of the scientific community over the last years is…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
Arboreal networks are multi-rooted phylogenetic networks whose underlying graph is a tree. We give an encoding of stack-free arboreal networks in terms of triplets and the novel concept of a duet. This yields a polynomial time algorithm to…
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…
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,…
We present the first sublinear-time algorithm for a distributed message-passing network sto compute its edge connectivity $\lambda$ exactly in the CONGEST model, as long as there are no parallel edges. Our algorithm takes $\tilde…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
Most phylogenetic analyses result in a sample of trees, but summarizing and visualizing these samples can be challenging. Consensus trees often provide limited information about a sample, and so methods such as consensus networks,…
We give a greedy learning algorithm for reconstructing an evolutionary tree based on a certain harmonic average on triplets of terminal taxa. After the pairwise distances between terminal taxa are estimated from sequence data, the algorithm…
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…
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…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
The need for structures capable of accommodating complex evolutionary signals such as those found in, for example, wheat has fueled research into phylogenetic networks. Such structures generalize the standard phylogenetic tree model by also…
We derive a quadratic-time algorithm for the genus distribution of any 3-regular, biconnected series-parallel graph, which we extend to any biconnected series-parallel graph of maximum degree at most 3. Since the biconnected components of…
Towards the vision of translating code that implements an algorithm from one programming language into another, this paper proposes an approach for automated program classification using bilateral tree-based convolutional neural networks…