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BIO::Phylo-phyloinformatic analysis using perl
BACKGROUND: Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2011
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056726/ https://www.ncbi.nlm.nih.gov/pubmed/21352572 http://dx.doi.org/10.1186/1471-2105-12-63 |
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author | Vos, Rutger A Caravas, Jason Hartmann, Klaas Jensen, Mark A Miller, Chase |
author_facet | Vos, Rutger A Caravas, Jason Hartmann, Klaas Jensen, Mark A Miller, Chase |
author_sort | Vos, Rutger A |
collection | PubMed |
description | BACKGROUND: Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. RESULTS: This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. CONCLUSIONS: Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo |
format | Text |
id | pubmed-3056726 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2011 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-30567262011-03-15 BIO::Phylo-phyloinformatic analysis using perl Vos, Rutger A Caravas, Jason Hartmann, Klaas Jensen, Mark A Miller, Chase BMC Bioinformatics Software BACKGROUND: Phyloinformatic analyses involve large amounts of data and metadata of complex structure. Collecting, processing, analyzing, visualizing and summarizing these data and metadata should be done in steps that can be automated and reproduced. This requires flexible, modular toolkits that can represent, manipulate and persist phylogenetic data and metadata as objects with programmable interfaces. RESULTS: This paper presents Bio::Phylo, a Perl5 toolkit for phyloinformatic analysis. It implements classes and methods that are compatible with the well-known BioPerl toolkit, but is independent from it (making it easy to install) and features a richer API and a data model that is better able to manage the complex relationships between different fundamental data and metadata objects in phylogenetics. It supports commonly used file formats for phylogenetic data including the novel NeXML standard, which allows rich annotations of phylogenetic data to be stored and shared. Bio::Phylo can interact with BioPerl, thereby giving access to the file formats that BioPerl supports. Many methods for data simulation, transformation and manipulation, the analysis of tree shape, and tree visualization are provided. CONCLUSIONS: Bio::Phylo is composed of 59 richly documented Perl5 modules. It has been deployed successfully on a variety of computer architectures (including various Linux distributions, Mac OS X versions, Windows, Cygwin and UNIX-like systems). It is available as open source (GPL) software from http://search.cpan.org/dist/Bio-Phylo BioMed Central 2011-02-27 /pmc/articles/PMC3056726/ /pubmed/21352572 http://dx.doi.org/10.1186/1471-2105-12-63 Text en Copyright © 2011 Vos et al; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Vos, Rutger A Caravas, Jason Hartmann, Klaas Jensen, Mark A Miller, Chase BIO::Phylo-phyloinformatic analysis using perl |
title | BIO::Phylo-phyloinformatic analysis using perl |
title_full | BIO::Phylo-phyloinformatic analysis using perl |
title_fullStr | BIO::Phylo-phyloinformatic analysis using perl |
title_full_unstemmed | BIO::Phylo-phyloinformatic analysis using perl |
title_short | BIO::Phylo-phyloinformatic analysis using perl |
title_sort | bio::phylo-phyloinformatic analysis using perl |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3056726/ https://www.ncbi.nlm.nih.gov/pubmed/21352572 http://dx.doi.org/10.1186/1471-2105-12-63 |
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