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BIO::Phylo-phyloinformatic analysis using Perl


Vos, RA and Caravas, J and Hartmann, K and Jensen, MA and Miller, C, BIO::Phylo-phyloinformatic analysis using Perl, BMC Bioinformatics, 12, (63) pp. 1-9. ISSN 1471-2105 (2011) [Refereed Article]


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Creative Commons Attribution License © 1999-2011 BioMed Central Ltd

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DOI: doi:10.1186/1471-2105-12-63


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

Item Details

Item Type:Refereed Article
Research Division:Biological Sciences
Research Group:Evolutionary biology
Research Field:Phylogeny and comparative analysis
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the biological sciences
UTAS Author:Hartmann, K (Dr Klaas Hartmann)
ID Code:71106
Year Published:2011
Web of Science® Times Cited:29
Deposited By:Sustainable Marine Research Collaboration
Deposited On:2011-07-07
Last Modified:2018-04-16
Downloads:399 View Download Statistics

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