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The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data
The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low boo...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850655/ https://www.ncbi.nlm.nih.gov/pubmed/28100791 http://dx.doi.org/10.1093/molbev/msw272 |
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author | Katsura, Yukako Stanley, Craig E. Kumar, Sudhir Nei, Masatoshi |
author_facet | Katsura, Yukako Stanley, Craig E. Kumar, Sudhir Nei, Masatoshi |
author_sort | Katsura, Yukako |
collection | PubMed |
description | The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented. |
format | Online Article Text |
id | pubmed-5850655 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58506552018-03-23 The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data Katsura, Yukako Stanley, Craig E. Kumar, Sudhir Nei, Masatoshi Mol Biol Evol Discoveries The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented. Oxford University Press 2017-03 2017-01-18 /pmc/articles/PMC5850655/ /pubmed/28100791 http://dx.doi.org/10.1093/molbev/msw272 Text en © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. 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 reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Discoveries Katsura, Yukako Stanley, Craig E. Kumar, Sudhir Nei, Masatoshi The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title | The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title_full | The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title_fullStr | The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title_full_unstemmed | The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title_short | The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data |
title_sort | reliability and stability of an inferred phylogenetic tree from empirical data |
topic | Discoveries |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850655/ https://www.ncbi.nlm.nih.gov/pubmed/28100791 http://dx.doi.org/10.1093/molbev/msw272 |
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