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van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)
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....
journal article 2020
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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, 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...
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
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Janssen, R. (author)
doctoral thesis 2021
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Huber, Katharina T. (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, V.L. (author), Murakami, Yukihiro (author), Semple, Charles (author)
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....
journal article 2024
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Deen, Elise (author), van Iersel, L.J.J. (author), Janssen, Remie (author), Jones, M.E.L. (author), Murakami, Yukihiro (author), Zeh, Norbert (author)
The maximum parsimony distance d<sub>MP</sub>(T<sub>1</sub>,T<sub>2</sub>) and the bounded-state maximum parsimony distance d<sub>MP</sub><sup>t</sup>(T<sub>1</sub>,T<sub>2</sub>) measure the difference between two phylogenetic trees T<sub>1</sub>,T<sub>2</sub> in terms of the maximum difference between their parsimony scores for any...
journal article 2024
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