Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data

SUMMARY: We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level...

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Detalles Bibliográficos
Autores principales: Czech, Lucas, Barbera, Pierre, Stamatakis, Alexandros
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214027/
https://www.ncbi.nlm.nih.gov/pubmed/32016344
http://dx.doi.org/10.1093/bioinformatics/btaa070
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author Czech, Lucas
Barbera, Pierre
Stamatakis, Alexandros
author_facet Czech, Lucas
Barbera, Pierre
Stamatakis, Alexandros
author_sort Czech, Lucas
collection PubMed
description SUMMARY: We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven. AVAILABILITY AND IMPLEMENTATION: Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-72140272020-05-15 Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data Czech, Lucas Barbera, Pierre Stamatakis, Alexandros Bioinformatics Applications Notes SUMMARY: We present genesis, a library for working with phylogenetic data, and gappa, an accompanying command-line tool for conducting typical analyses on such data. The tools target phylogenetic trees and phylogenetic placements, sequences, taxonomies and other relevant data types, offer high-level simplicity as well as low-level customizability, and are computationally efficient, well-tested and field-proven. AVAILABILITY AND IMPLEMENTATION: Both genesis and gappa are written in modern C++11, and are freely available under GPLv3 at http://github.com/lczech/genesis and http://github.com/lczech/gappa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2020-05-15 2020-02-04 /pmc/articles/PMC7214027/ /pubmed/32016344 http://dx.doi.org/10.1093/bioinformatics/btaa070 Text en © The Author(s) 2020. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Czech, Lucas
Barbera, Pierre
Stamatakis, Alexandros
Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title_full Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title_fullStr Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title_full_unstemmed Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title_short Genesis and Gappa: processing, analyzing and visualizing phylogenetic (placement) data
title_sort genesis and gappa: processing, analyzing and visualizing phylogenetic (placement) data
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7214027/
https://www.ncbi.nlm.nih.gov/pubmed/32016344
http://dx.doi.org/10.1093/bioinformatics/btaa070
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