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Visualizing incompatibilities in phylogenetic trees using consensus outlines
Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis. A consensus tree is often used to summarize what the trees have in common. Consensus networks were introduced to also allow t...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267324/ https://www.ncbi.nlm.nih.gov/pubmed/37325772 http://dx.doi.org/10.3389/fbinf.2023.1155286 |
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author | Huson, Daniel H. Cetinkaya, Banu |
author_facet | Huson, Daniel H. Cetinkaya, Banu |
author_sort | Huson, Daniel H. |
collection | PubMed |
description | Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis. A consensus tree is often used to summarize what the trees have in common. Consensus networks were introduced to also allow the visualization of the main incompatibilities among the trees. However, in practice, such networks often contain a large number of nodes and edges, and can be non-planar, making them difficult to interpret. Here, we introduce the new concept of a phylogenetic consensus outline, which provides a planar visualization of incompatibilities in the input trees, without the complexities of a consensus network. Furthermore, we present an effective algorithm for its computation. We demonstrate its usage and explore how it compares to other methods on a Bayesian phylogenetic analysis of languages using data from a published database and on multiple gene trees from a published study on water lilies. |
format | Online Article Text |
id | pubmed-10267324 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-102673242023-06-15 Visualizing incompatibilities in phylogenetic trees using consensus outlines Huson, Daniel H. Cetinkaya, Banu Front Bioinform Bioinformatics Phylogenetic analysis frequently leads to the creation of many phylogenetic trees, either from using multiple genes or methods, or through bootstrapping or Bayesian analysis. A consensus tree is often used to summarize what the trees have in common. Consensus networks were introduced to also allow the visualization of the main incompatibilities among the trees. However, in practice, such networks often contain a large number of nodes and edges, and can be non-planar, making them difficult to interpret. Here, we introduce the new concept of a phylogenetic consensus outline, which provides a planar visualization of incompatibilities in the input trees, without the complexities of a consensus network. Furthermore, we present an effective algorithm for its computation. We demonstrate its usage and explore how it compares to other methods on a Bayesian phylogenetic analysis of languages using data from a published database and on multiple gene trees from a published study on water lilies. Frontiers Media S.A. 2023-06-01 /pmc/articles/PMC10267324/ /pubmed/37325772 http://dx.doi.org/10.3389/fbinf.2023.1155286 Text en Copyright © 2023 Huson and Cetinkaya. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Bioinformatics Huson, Daniel H. Cetinkaya, Banu Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title | Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title_full | Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title_fullStr | Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title_full_unstemmed | Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title_short | Visualizing incompatibilities in phylogenetic trees using consensus outlines |
title_sort | visualizing incompatibilities in phylogenetic trees using consensus outlines |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10267324/ https://www.ncbi.nlm.nih.gov/pubmed/37325772 http://dx.doi.org/10.3389/fbinf.2023.1155286 |
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