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A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees

For each given pair of (rooted or unrooted) topological trees with the same number of leaves a strict upper bound is shown for the tree partition distance (also called symmetric difference metric and Robinson-Foulds distance)—in case of unrooted trees—and for the cluster distance (also called Robins...

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Autores principales: Middendorf, Martin, Wieseke, Nicolas
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161905/
https://www.ncbi.nlm.nih.gov/pubmed/30265723
http://dx.doi.org/10.1371/journal.pone.0204907
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author Middendorf, Martin
Wieseke, Nicolas
author_facet Middendorf, Martin
Wieseke, Nicolas
author_sort Middendorf, Martin
collection PubMed
description For each given pair of (rooted or unrooted) topological trees with the same number of leaves a strict upper bound is shown for the tree partition distance (also called symmetric difference metric and Robinson-Foulds distance)—in case of unrooted trees—and for the cluster distance (also called Robinson-Foulds distance)—in case of rooted trees—of corresponding phylogenetic trees. In particular, it is shown that there exist assignments of labels (e.g., species) to the leaves of both topological tree where each label is assigned to exactly one leaf in each tree such that: i) in the unrooted case, the tree partition distance between the corresponding phylogenetic trees equals the number of internal edges in both trees minus the number of nodes with degree 2 in both trees, ii) in the rooted case, the cluster distance between any two corresponding phylogenetic trees equals the number of internal edges in both trees minus the number of nodes with degree 2 in both trees, and iii) the values in (i) and (ii) are also the maximum values with respect to all possible assignments. The shown strict worst case bounds are needed as normalization factor to compute a normalized version of the respective tree partition metrics.
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spelling pubmed-61619052018-10-19 A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees Middendorf, Martin Wieseke, Nicolas PLoS One Research Article For each given pair of (rooted or unrooted) topological trees with the same number of leaves a strict upper bound is shown for the tree partition distance (also called symmetric difference metric and Robinson-Foulds distance)—in case of unrooted trees—and for the cluster distance (also called Robinson-Foulds distance)—in case of rooted trees—of corresponding phylogenetic trees. In particular, it is shown that there exist assignments of labels (e.g., species) to the leaves of both topological tree where each label is assigned to exactly one leaf in each tree such that: i) in the unrooted case, the tree partition distance between the corresponding phylogenetic trees equals the number of internal edges in both trees minus the number of nodes with degree 2 in both trees, ii) in the rooted case, the cluster distance between any two corresponding phylogenetic trees equals the number of internal edges in both trees minus the number of nodes with degree 2 in both trees, and iii) the values in (i) and (ii) are also the maximum values with respect to all possible assignments. The shown strict worst case bounds are needed as normalization factor to compute a normalized version of the respective tree partition metrics. Public Library of Science 2018-09-28 /pmc/articles/PMC6161905/ /pubmed/30265723 http://dx.doi.org/10.1371/journal.pone.0204907 Text en © 2018 Middendorf, Wieseke http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Middendorf, Martin
Wieseke, Nicolas
A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title_full A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title_fullStr A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title_full_unstemmed A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title_short A strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
title_sort strict upper bound for the partition distance and the cluster distance of phylogenetic trees for each fixed pair of topological trees
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6161905/
https://www.ncbi.nlm.nih.gov/pubmed/30265723
http://dx.doi.org/10.1371/journal.pone.0204907
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