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SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees
BACKGROUND: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the ta...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622420/ https://www.ncbi.nlm.nih.gov/pubmed/28964270 http://dx.doi.org/10.1186/s12859-017-1841-3 |
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author | Beccati, Alan Gerken, Jan Quast, Christian Yilmaz, Pelin Glöckner, Frank Oliver |
author_facet | Beccati, Alan Gerken, Jan Quast, Christian Yilmaz, Pelin Glöckner, Frank Oliver |
author_sort | Beccati, Alan |
collection | PubMed |
description | BACKGROUND: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. RESULTS: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. CONCLUSIONS: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself. |
format | Online Article Text |
id | pubmed-5622420 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-56224202017-10-11 SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees Beccati, Alan Gerken, Jan Quast, Christian Yilmaz, Pelin Glöckner, Frank Oliver BMC Bioinformatics Software BACKGROUND: Phylogenetic trees are an important tool to study the evolutionary relationships among organisms. The huge amount of available taxa poses difficulties in their interactive visualization. This hampers the interaction with the users to provide feedback for the further improvement of the taxonomic framework. RESULTS: The SILVA Tree Viewer is a web application designed for visualizing large phylogenetic trees without requiring the download of any software tool or data files. The SILVA Tree Viewer is based on Web Geographic Information Systems (Web-GIS) technology with a PostgreSQL backend. It enables zoom and pan functionalities similar to Google Maps. The SILVA Tree Viewer enables access to two phylogenetic (guide) trees provided by the SILVA database: the SSU Ref NR99 inferred from high-quality, full-length small subunit sequences, clustered at 99% sequence identity and the LSU Ref inferred from high-quality, full-length large subunit sequences. CONCLUSIONS: The Tree Viewer provides tree navigation, search and browse tools as well as an interactive feedback system to collect any kinds of requests ranging from taxonomy to data curation and improving the tool itself. BioMed Central 2017-09-30 /pmc/articles/PMC5622420/ /pubmed/28964270 http://dx.doi.org/10.1186/s12859-017-1841-3 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Beccati, Alan Gerken, Jan Quast, Christian Yilmaz, Pelin Glöckner, Frank Oliver SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title | SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title_full | SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title_fullStr | SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title_full_unstemmed | SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title_short | SILVA tree viewer: interactive web browsing of the SILVA phylogenetic guide trees |
title_sort | silva tree viewer: interactive web browsing of the silva phylogenetic guide trees |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5622420/ https://www.ncbi.nlm.nih.gov/pubmed/28964270 http://dx.doi.org/10.1186/s12859-017-1841-3 |
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