Bio.Phylo: A Unified Toolkit for Processing, Analyzing and Visualizing Phylogenetic Trees in Biopython

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Bio.Phylo: A Unified Toolkit for Processing, Analyzing and Visualizing Phylogenetic Trees in Biopython

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Title: Bio.Phylo: A Unified Toolkit for Processing, Analyzing and Visualizing Phylogenetic Trees in Biopython
Author: Talevich, Eric; Invergo, Brandon M; Cock, Peter JA; Chapman, Brad Alan

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Citation: Talevich, Eric, Brandon M. Invergo, Peter J. A. Cock, and Brad A. Chapman. 2012. Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. BMC Bioinformatics 13:209.
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Abstract: Background: Ongoing innovation in phylogenetics and evolutionary biology has been accompanied by a proliferation of software tools, data formats, analytical techniques and web servers. This brings with it the challenge of integrating phylogenetic and other related biological data found in a wide variety of formats, and underlines the need for reusable software that can read, manipulate and transform this information into the various forms required to build computational pipelines. Results: We built a Python software library for working with phylogenetic data that is tightly integrated with Biopython, a broad-ranging toolkit for computational biology. Our library, Bio.Phylo, is highly interoperable with existing libraries, tools and standards, and is capable of parsing common file formats for phylogenetic trees, performing basic transformations and manipulations, attaching rich annotations, and visualizing trees. We unified the modules for working with the standard file formats Newick, NEXUS and phyloXML behind a consistent and simple API, providing a common set of functionality independent of the data source. Conclusions: Bio.Phylo meets a growing need in bioinformatics for working with heterogeneous types of phylogenetic data. By supporting interoperability with multiple file formats and leveraging existing Biopython features, this library simplifies the construction of phylogenetic workflows. We also provide examples of the benefits of building a community around a shared open-source project. Bio.Phylo is included with Biopython, available through the Biopython website, http://biopython.org.
Published Version: doi:10.1186/1471-2105-13-209
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468381/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:10579671
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