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A new resolution function to evaluate tree shape statistics

Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed to investigate the shape of a phylogenetic tre...

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Detalles Bibliográficos
Autores principales: Hayati, Maryam, Shadgar, Bita, Chindelevitch, Leonid
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874070/
https://www.ncbi.nlm.nih.gov/pubmed/31751352
http://dx.doi.org/10.1371/journal.pone.0224197
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author Hayati, Maryam
Shadgar, Bita
Chindelevitch, Leonid
author_facet Hayati, Maryam
Shadgar, Bita
Chindelevitch, Leonid
author_sort Hayati, Maryam
collection PubMed
description Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed to investigate the shape of a phylogenetic tree. Tree shape statistics are a common approach to quantifying the shape of a phylogenetic tree by encoding it with a single number. In this article, we propose a new resolution function to evaluate the power of different tree shape statistics to distinguish between dissimilar trees. We show that the new resolution function requires less time and space in comparison with the previously proposed resolution function for tree shape statistics. We also introduce a new class of tree shape statistics, which are linear combinations of two existing statistics that are optimal with respect to a resolution function, and show evidence that the statistics in this class converge to a limiting linear combination as the size of the tree increases. Our implementation is freely available at https://github.com/WGS-TB/TreeShapeStats.
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spelling pubmed-68740702019-12-07 A new resolution function to evaluate tree shape statistics Hayati, Maryam Shadgar, Bita Chindelevitch, Leonid PLoS One Research Article Phylogenetic trees are frequently used in biology to study the relationships between a number of species or organisms. The shape of a phylogenetic tree contains useful information about patterns of speciation and extinction, so powerful tools are needed to investigate the shape of a phylogenetic tree. Tree shape statistics are a common approach to quantifying the shape of a phylogenetic tree by encoding it with a single number. In this article, we propose a new resolution function to evaluate the power of different tree shape statistics to distinguish between dissimilar trees. We show that the new resolution function requires less time and space in comparison with the previously proposed resolution function for tree shape statistics. We also introduce a new class of tree shape statistics, which are linear combinations of two existing statistics that are optimal with respect to a resolution function, and show evidence that the statistics in this class converge to a limiting linear combination as the size of the tree increases. Our implementation is freely available at https://github.com/WGS-TB/TreeShapeStats. Public Library of Science 2019-11-21 /pmc/articles/PMC6874070/ /pubmed/31751352 http://dx.doi.org/10.1371/journal.pone.0224197 Text en © 2019 Hayati et al 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
Hayati, Maryam
Shadgar, Bita
Chindelevitch, Leonid
A new resolution function to evaluate tree shape statistics
title A new resolution function to evaluate tree shape statistics
title_full A new resolution function to evaluate tree shape statistics
title_fullStr A new resolution function to evaluate tree shape statistics
title_full_unstemmed A new resolution function to evaluate tree shape statistics
title_short A new resolution function to evaluate tree shape statistics
title_sort new resolution function to evaluate tree shape statistics
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874070/
https://www.ncbi.nlm.nih.gov/pubmed/31751352
http://dx.doi.org/10.1371/journal.pone.0224197
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