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Orienting undirected phylogenetic networks

Authors: Katharina T. Huber; Leo van Iersel; Remie Janssen; Mark Jones 0001; Vincent Moulton; Yukihiro Murakami; Charles Semple;

Orienting undirected phylogenetic networks

Abstract

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. Moreover, we characterize when this is possible and show that, in such instances, the resulting directed nonbinary phylogenetic network is unique. In addition, without being given the location of the root and the reticulation vertices, we describe an algorithm for deciding whether an undirected binary phylogenetic network $N$ can be oriented as a directed binary phylogenetic network of a certain class. The algorithm is fixed-parameter tractable (FPT) when the parameter is the level of $N$ and is applicable to classes of directed phylogenetic networks that satisfy certain conditions. As an example, we show that the well-studied class of binary tree-child networks satisfies these conditions.

contains an appendix with additional results not presented in the journal version

Countries
United Kingdom, Netherlands
Keywords

FOS: Computer and information sciences, Characterization, phylogenetic network, Polynomial-time algorithm, Computational biology, computational biology, graph algorithm, Computer Science - Data Structures and Algorithms, FOS: Mathematics, Mathematics - Combinatorics, characterization, Data Structures and Algorithms (cs.DS), Quantitative Biology - Populations and Evolution, graph orientation, Phylogenetic network, 000, Graph algorithm, polynomial-time algorithm, Populations and Evolution (q-bio.PE), Computer science, 004, Phylogenetics, phylogenetics, Fixed-parameter tractability, fixed-parameter tractability, FOS: Biological sciences, Combinatorics (math.CO), Graph orientation

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
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