3 citations · 8 across the 23 of their papers we have counts for
25 papers
How many cherry-picking sequences are needed to reduce all subtrees of a phylogenetic tree?
Bálint Kollmann, Yukihiro Murakami, Takatora Suzuki
Phylogenetic networks are graphs that represent the evolutionary history of species. Recently, the class of orchard phylogenetic networks, which can be reduced by so-called cherry-…
Metropolis-Hastings Sampling of Phylogenetic Networks: Correcting for Symmetries
Leo van Iersel, Remie Janssen, Mark Jones +2
In phylogenetics, Metropolis-Hastings methods are commonly used to sample phylogenetic trees or networks, for example from Bayesian posteriors. These methods generally use transiti…
Proximity Measures for Classes of Phylogenetic Networks
Leo van Iersel, Mark Jones, Esther Julien +2
Phylogenetic networks are used to represent the evolutionary history of species. Due to biological interpretations and computational advantages, researchers have focused on restric…
List -coloring -free graphs of diameter- in polynomial-time
Yukihiro Murakami
We show that list -coloring a~-free graph of diameter- can be done in polynomial-time. Our algorithm is based on a structural characterization showing that many such gra…
Note on the Maximum Number of Trees Displayed by a Tree-Child Network
Yukihiro Murakami, Charles Semple
In this note, we show that, for all , the number of distinct rooted binary phylogenetic -trees displayed by a binary tree-child network on with lea…
Burning Graph Powers and Branching Trees
Jesper Jansson, Shashanka Kulamarva, Yukihiro Murakami +1
Graph burning is a discrete-time process that models the spread of social contagion. Initially, all vertices are unburned. In each round, one unburned vertex is selected and burned…
Metrics for classes of semi-binary phylogenetic networks using -representations
Christopher Reichling, Leo van Iersel, Yukihiro Murakami
Phylogenetic networks are useful in representing the evolutionary history of taxa. In certain scenarios, one requires a way to compare different networks. In practice, this can be…
A Wild Sheep Chase Through an Orchard
Jordan Dempsey, Leo van Iersel, Mark Jones +2
Orchards are a biologically relevant class of phylogenetic networks as they can describe treelike evolutionary histories augmented with horizontal transfer events. Moreover, the cl…
Fence decompositions and cherry covers in non-binary phylogenetic networks
Joan Carles Pons, Pau Vives López, Yukihiro Murakami +1
Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained emin…
Orienting undirected phylogenetic networks to tree-child network
Shunsuke Maeda, Yusuke Kaneko, Hideaki Muramatsu +2
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 ev…
Making a Network Orchard by Adding Leaves
Leo van Iersel, Mark Jones, Esther Julien +1
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 interpreta…
A Near-Linear Kernel for Two-Parsimony Distance
Elise Deen, Leo van Iersel, Remie Janssen +3
The maximum parsimony distance and the bounded-state maximum parsimony distance measure the difference between two phylogene…
Polynomial invariants for cactuses
Leo van Iersel, Vincent Moulton, Yukihiro Murakami
Graph invariants are a useful tool in graph theory. Not only do they encode useful information about the graphs to which they are associated, but complete invariants can be used to…
Orchard Networks are Trees with Additional Horizontal Arcs
Leo van Iersel, Remie Janssen, Mark Jones +1
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits,…
Level- networks from shortest and longest distances
Katharina T. Huber, Leo van Iersel, Remie Janssen +3
Recently it was shown that a certain class of phylogenetic networks, called level- networks, cannot be reconstructed from their associated distance matrices. In this paper, we s…
Distinguishing level-1 phylogenetic networks on the basis of data generated by Markov processes
Elizabeth Gross, Leo van Iersel, Remie Janssen +3
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such a…
A Unifying Characterization of Tree-based Networks and Orchard Networks using Cherry Covers
Leo van Iersel, Remie Janssen, Mark Jones +2
Phylogenetic networks are used to study evolutionary relationships between species in biology. Such networks are often categorized into classes by their topological features, which…
Combining Networks using Cherry Picking Sequences
Remie Janssen, Mark Jones, Yukihiro Murakami
Phylogenetic networks are important for the study of evolution. The number of methods to find such networks is increasing, but most such methods can only reconstruct small networks…
Reconstructibility of unrooted level- phylogenetic networks from distances
Leo van Iersel, Vincent Moulton, Yukihiro Murakami
A phylogenetic network is a graph-theoretical tool that is used by biologists to represent the evolutionary history of a collection of species. One potential way of constructing su…
Recognizing and realizing cactus metrics
Momoko Hayamizu, Katharina T. Huber, Vincent Moulton +1
The problem of realizing finite metric spaces in terms of weighted graphs has many applications. For example, the mathematical and computational properties of metrics that can be r…
A Practical Fixed-Parameter Algorithm for Constructing Tree-Child Networks from Multiple Binary Trees
Leo van Iersel, Remie Janssen, Mark Jones +2
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number…
Orienting undirected phylogenetic networks
Katharina T. Huber, Leo van Iersel, Remie Janssen +4
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undir…
On Cherry-picking and Network Containment
Remie Janssen, Yukihiro Murakami
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…
Reconstructing Tree-Child Networks from Reticulate-Edge-Deleted Subnetworks
Yukihiro Murakami, Leo van Iersel, Remie Janssen +2
Network reconstruction lies at the heart of phylogenetic research. Two well studied classes of phylogenetic networks include tree-child networks and level- networks. In a tree-c…