research-article

A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks

Authors:

Mercè Llabrés,

Francesc Rosselló,

Gabriel ValienteAuthors Info & Claims

BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Article No.: 13, Pages 1 - 10

https://doi.org/10.1145/3388440.3412479

Published: 10 November 2020 Publication History

Abstract

Cancer evolution is often modeled by clonal trees (whose nodes are labeled by multiple somatic mutations) or mutation trees (where nodes are labeled by single somatic mutations). Clonal trees are generated from sequence data with different computational methods that may produce different clone phylogenies, rendering their analysis and comparison necessary to infer mutation order and clone origin during tumor progression. In this paper, we present a distance metric for multi-labeled trees that generalizes the Robinson-Foulds distance for phylogenetic trees, allows for a similarity assessment at much higher resolution, and can be applied to trees and networks with different sets of node labels. The generalized Robinson-Foulds distance can be computed in time quadratic in the size of the input multisets of multisets of node labels, and is a metric for clonal trees, mutation trees, phylogenetic trees, and several classes of phylogenetic networks.

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Cited By

Farnia MTahiri N(2024)New generalized metric based on branch length distance to compare B cell lineage treesAlgorithms for Molecular Biology10.1186/s13015-024-00267-119:1Online publication date: 5-Oct-2024
https://doi.org/10.1186/s13015-024-00267-1
Khayatian EValiente GZhang L(2023)The K-Robinson Foulds Measures for Labeled TreesComparative Genomics10.1007/978-3-031-36911-7_10(146-161)Online publication date: 13-Jul-2023
https://doi.org/10.1007/978-3-031-36911-7_10
Pit-Claudel CLämmel RTratt Lde Lara J(2020)Untangling mechanized proofsProceedings of the 13th ACM SIGPLAN International Conference on Software Language Engineering10.1145/3426425.3426940(155-174)Online publication date: 16-Nov-2020
https://dl.acm.org/doi/10.1145/3426425.3426940

Index Terms

A Generalized Robinson-Foulds Distance for Clonal Trees, Mutation Trees, and Phylogenetic Trees and Networks
1. Applied computing
  1. Life and medical sciences
    1. Bioinformatics
    2. Computational biology
      1. Molecular evolution

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BCB '20: Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

September 2020

193 pages

ISBN:9781450379649

DOI:10.1145/3388440

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Cited By

Farnia MTahiri N(2024)New generalized metric based on branch length distance to compare B cell lineage treesAlgorithms for Molecular Biology10.1186/s13015-024-00267-119:1Online publication date: 5-Oct-2024
https://doi.org/10.1186/s13015-024-00267-1
Khayatian EValiente GZhang L(2023)The K-Robinson Foulds Measures for Labeled TreesComparative Genomics10.1007/978-3-031-36911-7_10(146-161)Online publication date: 13-Jul-2023
https://doi.org/10.1007/978-3-031-36911-7_10
Pit-Claudel CLämmel RTratt Lde Lara J(2020)Untangling mechanized proofsProceedings of the 13th ACM SIGPLAN International Conference on Software Language Engineering10.1145/3426425.3426940(155-174)Online publication date: 16-Nov-2020
https://dl.acm.org/doi/10.1145/3426425.3426940

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