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DOI: 10.4230/LIPIcs.WABI.2023.7

Making a Network Orchard by Adding Leaves

Authors: Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami

Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)

Abstract

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 interpretable as trees with additional horizontal arcs. This makes the network class ideal for capturing evolutionary histories that involve horizontal gene transfers. Here, we study the minimum number of additional leaves needed to make a network orchard. We demonstrate that computing this proximity measure for a given network is NP-hard and describe a tight upper bound. We also give an equivalent measure based on vertex labellings to construct a mixed integer linear programming formulation. Our experimental results, which include both real-world and synthetic data, illustrate the efficiency of our implementation.

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Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami. Making a Network Orchard by Adding Leaves. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 7:1-7:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{vaniersel_et_al:LIPIcs.WABI.2023.7,
  author =	{van Iersel, Leo and Jones, Mark and Julien, Esther and Murakami, Yukihiro},
  title =	{{Making a Network Orchard by Adding Leaves}},
  booktitle =	{23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)},
  pages =	{7:1--7:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-294-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{273},
  editor =	{Belazzougui, Djamal and Ouangraoua, A\"{i}da},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.7},
  URN =		{urn:nbn:de:0030-drops-186333},
  doi =		{10.4230/LIPIcs.WABI.2023.7},
  annote =	{Keywords: Phylogenetics, Network, Orchard Networks, Proximity Measures, NP-hardness}
}

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Making a Network Orchard by Adding Leaves

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