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

Llabrés, Mercè; Rosselló, Francesc; Valiente, Gabriel

doi:10.1145/3388440.3412479

Cited by 8 publications

(16 citation statements)

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“…In the original formulation, the GRF distance allowed for comparing any structures that can be described by sets or multisets of sets of multisets of labels (Llabrés et al, 2020 ). When restricted to phylogenetic trees (with possibly different sets of taxa), which are described by sets of sets of taxa, the GRF distance is defined as follows.…”

Section: The Grf Distancementioning

confidence: 99%

“…Let T 1 and T 2 be phylogenetic trees, let

, and let

. The cluster representation of T 1 and T 2 can be obtained during a postorder traversal of the trees (Llabrés et al, 2020 , §2.2).…”

Section: The Grf Distancementioning

confidence: 99%

“…With a sorted list representation of the clusters, which uses

space and can be obtained in

time by radix sorting (Davis, 1992 ), and based on the idea behind the merge algorithm (Mehlhorn and Sanders, 2016 , §5.2) of the simultaneous traversal of two sorted lists or arrays, the union and the symmetric difference of two clusters can be computed in

time and thus, the GRF distance can be computed in

time using

space by a direct implementation of the formula in Definition 1. See Llabrés et al ( 2020 ) for details.…”

Section: The Grf Distancementioning

confidence: 99%

“…We have presented (Llabrés et al, 2020 ) a different generalization of the RF distance, based on the distances between sets of sets defined in Fujita ( 2013 ) and generalized to distances between multisets of multisets, which is a metric for the clonal trees (Govek et al, 2018 ; Karpov et al, 2019 ; DiNardo et al, 2020 ; Jahn et al, 2020 ) and the mutation trees (Kim and Simon, 2014 ; Aguse et al, 2019 ) that model tumor evolution under perfect phylogeny, phylogenetic trees, and several classes of phylogenetic networks, such as binary galled trees (Cardona et al, 2011 ), tree-child time-consistent phylogenetic networks (Cardona et al, 2008c , 2009a , b ), and semi-binary tree-sibling time-consistent phylogenetic networks (Cardona et al, 2008 a).…”

Section: Introductionmentioning

confidence: 99%

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The Generalized Robinson-Foulds Distance for Phylogenetic Trees

Llabrés

Rosselló

Valiente

2021

Journal of Computational Biology

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The Robinson-Foulds (RF) distance, one of the most widely used metrics for comparing phylogenetic trees, has the advantage of being intuitive, with a natural interpretation in terms of common splits, and it can be computed in linear time, but it has a very low resolution, and it may become trivial for phylogenetic trees with overlapping taxa, that is, phylogenetic trees that share some but not all of their leaf labels. In this article, we study the properties of the Generalized Robinson-Foulds (GRF) distance, a recently proposed metric for comparing any structures that can be described by multisets of multisets of labels, when applied to rooted phylogenetic trees with overlapping taxa, which are described by sets of clusters, that is, by sets of sets of labels. We show that the GRF distance has a very high resolution, it can also be computed in linear time, and it is not (uniformly) equivalent to the RF distance.

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Section: The Grf Distancementioning

confidence: 99%

“…Let T 1 and T 2 be phylogenetic trees, let

, and let

. The cluster representation of T 1 and T 2 can be obtained during a postorder traversal of the trees (Llabrés et al, 2020 , §2.2).…”

Section: The Grf Distancementioning

confidence: 99%

“…With a sorted list representation of the clusters, which uses

space and can be obtained in

time and thus, the GRF distance can be computed in

time using

space by a direct implementation of the formula in Definition 1. See Llabrés et al ( 2020 ) for details.…”

Section: The Grf Distancementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Generalized Robinson-Foulds Distance for Phylogenetic Trees

Llabrés

Rosselló

Valiente

2021

Journal of Computational Biology

Self Cite

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show abstract

“…Apart from the measures mentioned above, another recently proposed distance is the generalized RF distance (GRF) [13,14]. This measure allows for the comparison of phylogenetic trees, phylogenetic networks, mutation and clonal trees.…”

Section: Introductionmentioning

confidence: 99%

The k-RF Measures for Labeled Trees

Khayatian¹,

Valiente²,

Zhang³

2023

Preprint

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Investigating the mutational history of tumor cells is important for understanding the underlying mechanisms of cancer and its evolution. Now that the evolution of tumor cells is modeled using labeled trees, researchers are motivated to propose different measures for the comparison of mutation trees and other labeled trees. While the Robinson-Foulds distance is widely used for the comparison of phylogenetic trees, it has weaknesses when it is applied to labeled trees. Here, k-Robinson-Foulds dissimilarity measures are introduced for labeled tree comparison.

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