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BIO::Phylo-phyloinformatic analysis using perl

Rutger A Vos1*, Jason Caravas2, Klaas Hartmann3, Mark A Jensen4 and Chase Miller5

Author Affiliations

1 School of Biological Sciences, University of Reading, UK

2 Department of Biological Sciences, Wayne State University, Detroit, MI, USA

3 Tasmanian Aquaculture and Fisheries Institute, University of Tasmania, Australia

4 Fortinbras Research, Rockville, MD, USA

5 Center for Infection and Immunity, Columbia University, New York, NY, USA

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BMC Bioinformatics 2011, 12:63  doi:10.1186/1471-2105-12-63

Published: 27 February 2011

Abstract

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 webcite