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TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets
Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning o...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8857567/ https://www.ncbi.nlm.nih.gov/pubmed/35243369 http://dx.doi.org/10.1016/j.xpro.2022.101175 |
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author | Zhang, Xi Hu, Yining Eme, Laura Maruyama, Shinichiro Eveleigh, Robert J.M. Curtis, Bruce A. Sibbald, Shannon J. Hopkins, Julia F. Filloramo, Gina V. van Wijk, Klaas J. Archibald, John M. |
author_facet | Zhang, Xi Hu, Yining Eme, Laura Maruyama, Shinichiro Eveleigh, Robert J.M. Curtis, Bruce A. Sibbald, Shannon J. Hopkins, Julia F. Filloramo, Gina V. van Wijk, Klaas J. Archibald, John M. |
author_sort | Zhang, Xi |
collection | PubMed |
description | Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019). |
format | Online Article Text |
id | pubmed-8857567 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-88575672022-03-02 TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets Zhang, Xi Hu, Yining Eme, Laura Maruyama, Shinichiro Eveleigh, Robert J.M. Curtis, Bruce A. Sibbald, Shannon J. Hopkins, Julia F. Filloramo, Gina V. van Wijk, Klaas J. Archibald, John M. STAR Protoc Protocol Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019). Elsevier 2022-02-15 /pmc/articles/PMC8857567/ /pubmed/35243369 http://dx.doi.org/10.1016/j.xpro.2022.101175 Text en © 2022 The Author(s) https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Protocol Zhang, Xi Hu, Yining Eme, Laura Maruyama, Shinichiro Eveleigh, Robert J.M. Curtis, Bruce A. Sibbald, Shannon J. Hopkins, Julia F. Filloramo, Gina V. van Wijk, Klaas J. Archibald, John M. TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title | TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title_full | TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title_fullStr | TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title_full_unstemmed | TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title_short | TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
title_sort | treetuner: a pipeline for minimizing redundancy and complexity in large phylogenetic datasets |
topic | Protocol |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8857567/ https://www.ncbi.nlm.nih.gov/pubmed/35243369 http://dx.doi.org/10.1016/j.xpro.2022.101175 |
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