3 citations · 8 across the 23 of their papers we have counts for
15 papers · 1 filter
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-…
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…
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…
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…
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…
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…
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…