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SPECTRE: a suite of phylogenetic tools for reticulate evolution
SUMMARY: Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860355/ https://www.ncbi.nlm.nih.gov/pubmed/29186450 http://dx.doi.org/10.1093/bioinformatics/btx740 |
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author | Bastkowski, Sarah Mapleson, Daniel Spillner, Andreas Wu, Taoyang Balvočiūtė, Monika Moulton, Vincent |
author_facet | Bastkowski, Sarah Mapleson, Daniel Spillner, Andreas Wu, Taoyang Balvočiūtė, Monika Moulton, Vincent |
author_sort | Bastkowski, Sarah |
collection | PubMed |
description | SUMMARY: Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here, we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing environments. AVAILABILITY AND IMPLEMENTATION: Full source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE. SPECTRE’s core library is available from Maven Central at: https://mvnrepository.com/artifact/uk.ac.uea.cmp.spectre/core. Documentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
format | Online Article Text |
id | pubmed-5860355 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-58603552018-03-21 SPECTRE: a suite of phylogenetic tools for reticulate evolution Bastkowski, Sarah Mapleson, Daniel Spillner, Andreas Wu, Taoyang Balvočiūtė, Monika Moulton, Vincent Bioinformatics Applications Notes SUMMARY: Split-networks are a generalization of phylogenetic trees that have proven to be a powerful tool in phylogenetics. Various ways have been developed for computing such networks, including split-decomposition, NeighborNet, QNet and FlatNJ. Some of these approaches are implemented in the user-friendly SplitsTree software package. However, to give the user the option to adjust and extend these approaches and to facilitate their integration into analysis pipelines, there is a need for robust, open-source implementations of associated data structures and algorithms. Here, we present SPECTRE, a readily available, open-source library of data structures written in Java, that comes complete with new implementations of several pre-published algorithms and a basic interactive graphical interface for visualizing planar split networks. SPECTRE also supports the use of longer running algorithms by providing command line interfaces, which can be executed on servers or in High Performance Computing environments. AVAILABILITY AND IMPLEMENTATION: Full source code is available under the GPLv3 license at: https://github.com/maplesond/SPECTRE. SPECTRE’s core library is available from Maven Central at: https://mvnrepository.com/artifact/uk.ac.uea.cmp.spectre/core. Documentation is available at: http://spectre-suite-of-phylogenetic-tools-for-reticulate-evolution.readthedocs.io/en/latest/ SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2018-03-15 2017-11-24 /pmc/articles/PMC5860355/ /pubmed/29186450 http://dx.doi.org/10.1093/bioinformatics/btx740 Text en © The Author 2017. Published by Oxford University Press. 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 | Applications Notes Bastkowski, Sarah Mapleson, Daniel Spillner, Andreas Wu, Taoyang Balvočiūtė, Monika Moulton, Vincent SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title | SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title_full | SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title_fullStr | SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title_full_unstemmed | SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title_short | SPECTRE: a suite of phylogenetic tools for reticulate evolution |
title_sort | spectre: a suite of phylogenetic tools for reticulate evolution |
topic | Applications Notes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860355/ https://www.ncbi.nlm.nih.gov/pubmed/29186450 http://dx.doi.org/10.1093/bioinformatics/btx740 |
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