Orienting undirected phylogenetic networks

This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of the root and reticulation vertices, can be oriented as a directed nonbinary phylogenetic network....

A near-linear kernel for bounded-state parsimony distance

The maximum parsimony distance d_MP(T₁,T₂) and the bounded-state maximum parsimony distance d_MP^t(T₁,T₂) measure the difference between two phylogenetic trees T₁,T₂ in terms of the maximum difference between their parsimony scores for any...

Constructing phylogenetic networks via cherry picking and machine learning

Background: Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers of phylogenetic trees or are limited to severely restricted classes of networks. Results: In...

Making a Network Orchard by Adding Leaves

Phylogenetic networks are used to represent the evolutionary history of species. Recently, the new class of orchard networks was introduced, which were later shown to be interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here,...

Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning

Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. In this paper, we apply the recently-introduced theoretical framework of cherry picking to design a class of heuristics that are guaranteed to produce a network containing each of the input...

Rearranging Phylogenetic Networks

Heading in the right direction? Using head moves to traverse phylogenetic network space

Head moves are a type of rearrangement moves for phylogenetic net-works. They have primarily been studied as part of other types of moves, such as rSPR moves. Here, we study head moves as a type of moves on themselves. We show that the tiers (k > 0) of phylogenetic network space are connected by local head moves. Then, we show tail moves...

Maximum parsimony distance on phylogenetic trees: A linear kernel and constant factor approximation algorithm

Maximum parsimony distance is a measure used to quantify the dissimilarity of two unrooted phylogenetic trees. It is NP-hard to compute, and very few positive algorithmic results are known due to its complex combinatorial structure. Here we address this shortcoming by showing that the problem is fixed parameter tractable. We do this by...

A unifying characterization of tree-based networks and orchard networks using cherry covers

Phylogenetic networks are used to represent evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which stem from both biological and computational motivations. We study two network classes in this paper: tree-based networks and orchard networks. Tree-based...

Linear Time Algorithm for Tree-Child Network Containment

Phylogenetic networks are used to represent evolutionary scenarios in biology and linguistics. To find the most probable scenario, it may be necessary to compare candidate networks, to distinguish different networks, and to see when one network is embedded in another. Here, we consider the Network Containment problem, which asks whether a...

Polynomial-Time Algorithms for Phylogenetic Inference Problems Involving Duplication and Reticulation

A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree based on a model with speciation and duplication where duplications are clustered in duplication episodes....

Flavin-dependent N-hydroxylating enzymes: Distribution and application

Amino groups derived from naturally abundant amino acids or (di)amines can be used as “shuttles” in nature for oxygen transfer to provide intermediates or products comprising N-O functional groups such as N-hydroxy, oxazine, isoxazolidine, nitro, nitrone, oxime, C-, S-, or N-nitroso, and azoxy units. To this end, molecular oxygen is activated...

Deciding the existence of a cherry-picking sequence is hard on two trees

Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which proved hardness for eight or more trees. Via a known equivalence between cherry-picking sequences and...

Not all phylogenetic networks are leaf-reconstructible

Unrooted phylogenetic networks are graphs used to represent reticulate evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all unrooted phylogenetic networks for at least five taxa can be uniquely reconstructed from their subnetworks obtained...

Constructing a Consensus Phylogeny from a Leaf-Removal Distance: (Extended Abstract)