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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 of speciation and duplication where duplications are clustered in duplication episodes....
conference paper 2018
document
Janssen, R. (author), Jones, M.E.L. (author), Erdős, Péter L. (author), van Iersel, L.J.J. (author), Scornavacca, Celine (author)
Popular methods for exploring the space of rooted phylogenetic trees use rearrangement moves such as rooted Nearest Neighbour Interchange (rNNI) and rooted Subtree Prune and Regraft (rSPR). Recently, these moves were generalized to rooted phylogenetic networks, which are a more suitable representation of reticulate evolutionary histories, and...
journal article 2018
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van Ee, Martijn (author), van Iersel, L.J.J. (author), Janssen, T.M.L. (author), Sitters, René (author)
In this paper, we consider the a priori traveling salesman problem in the scenario model. In this problem, we are given a list of subsets of the vertices, called scenarios, along with a probability for each scenario. Given a tour on all vertices, the resulting tour for a given scenario is obtained by restricting the solution to the vertices...
journal article 2018
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Murakami, Yukihiro (author), van Iersel, L.J.J. (author), Janssen, R. (author), Jones, M.E.L. (author), Moulton, V.L. (author)
Network reconstruction lies at the heart of phylogenetic research. Two well-studied classes of phylogenetic networks include tree-child networks and level-k networks. In a tree-child network, every non-leaf node has a child that is a tree node or a leaf. In a level-k network, the maximum number of reticulations contained in a biconnected...
journal article 2019
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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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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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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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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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