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Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author)
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. To find bigger networks, one can attempt to combine small networks. In this paper, we study the Network Hybridization problem, a problem of combining networks...
conference paper 2020
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Janssen, R. (author)
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...
journal article 2021
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van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)
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...
journal article 2021
document
Janssen, R. (author), Murakami, Yukihiro (author)
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. In particular, one needs to distinguish different networks and determine whether one network is contained in another. In this paper, we introduce cherry-picking...
journal article 2021
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Gross, Elizabeth (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Long, Colby (author), Murakami, Yukihiro (author)
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees. These networks are able to incorporate reticulate evolutionary events such as hybridization, introgression, and lateral gene transfer. Recently, network-based Markov models of DNA sequence evolution have been introduced along with model...
journal article 2021
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Huber, Katharina T. (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, Vincent (author), Murakami, Yukihiro (author)
Recently it was shown that a certain class of phylogenetic networks, called level-2 networks, cannot be reconstructed from their associated distance matrices. In this paper, we show that they can be reconstructed from their induced shortest and longest distance matrices. That is, if two level-2 networks induce the same shortest and longest...
journal article 2022
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van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)
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 of reticulations among all such networks. The algorithm uses the recently introduced framework of cherry picking sequences and runs in O((8 k) <sup>k</sup>poly (n,...
journal article 2022
document
van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author)
Phylogenetic networks are used in biology to represent evolutionary histories. The class of orchard phylogenetic networks was recently introduced for their computational benefits, without any biological justification. Here, we show that orchard networks can be interpreted as trees with additional horizontal arcs. Therefore, they are closely...
journal article 2022
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