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SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees
We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embe...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
PeerJ Inc.
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012314/ https://www.ncbi.nlm.nih.gov/pubmed/27635331 http://dx.doi.org/10.7717/peerj.2359 |
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author | DeBlasio, Dan F. Wisecaver, Jennifer H. |
author_facet | DeBlasio, Dan F. Wisecaver, Jennifer H. |
author_sort | DeBlasio, Dan F. |
collection | PubMed |
description | We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/. |
format | Online Article Text |
id | pubmed-5012314 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | PeerJ Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-50123142016-09-15 SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees DeBlasio, Dan F. Wisecaver, Jennifer H. PeerJ Bioinformatics We present the phylogeny analysis software SICLE (Sister Clade Extractor), an easy-to-use, high-throughput tool to describe the nearest neighbors to a node of interest in a phylogenetic tree as well as the support value for the relationship. The application is a command line utility that can be embedded into a phylogenetic analysis pipeline or can be used as a subroutine within another C++ program. As a test case, we applied this new tool to the published phylome of Salinibacter ruber, a species of halophilic Bacteriodetes, identifying 13 unique sister relationships to S. ruber across the 4,589 gene phylogenies. S. ruber grouped with bacteria, most often other Bacteriodetes, in the majority of phylogenies, but 91 phylogenies showed a branch-supported sister association between S. ruber and Archaea, an evolutionarily intriguing relationship indicative of horizontal gene transfer. This test case demonstrates how SICLE makes it possible to summarize the phylogenetic information produced by automated phylogenetic pipelines to rapidly identify and quantify the possible evolutionary relationships that merit further investigation. SICLE is available for free for noncommercial use at http://eebweb.arizona.edu/sicle/. PeerJ Inc. 2016-08-23 /pmc/articles/PMC5012314/ /pubmed/27635331 http://dx.doi.org/10.7717/peerj.2359 Text en ©2016 DeBlasio and Wisecaver 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, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited. |
spellingShingle | Bioinformatics DeBlasio, Dan F. Wisecaver, Jennifer H. SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title |
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title_full |
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title_fullStr |
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title_full_unstemmed |
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title_short |
SICLE: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
title_sort | sicle: a high-throughput tool for extracting evolutionary relationships from phylogenetic trees |
topic | Bioinformatics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5012314/ https://www.ncbi.nlm.nih.gov/pubmed/27635331 http://dx.doi.org/10.7717/peerj.2359 |
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