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Bioinformatics Advance Access published online on March 20, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp163
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Biopython: freely available Python tools for computational molecular biology and bioinformatics

Peter J. A. Cock 1,*, Tiago Antao 2, Jeffrey T. Chang 3, Brad A. Chapman 4, Cymon J. Cox 5, Andrew Dalke 6, Iddo Friedberg 7, Thomas Hamelryck 8, Frank Kauff 9, Bartek Wilczynski 10 and Michiel J. L. de Hoon 11

1Plant Pathology, SCRI, Invergowrie, Dundee DD2 5DA, UK, 2Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK, 3Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC, USA, 4Department of Molecular Biology, Simches Research Center, Boston, MA 02114, USA, 5Centro de Ciências do Mar, Universidade do Algarve, Faro, Portugal, 6Andrew Dalke Scientific, AB, Gothenburg, Sweden, 7California Institute for Telecommunications and Information Technology, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0446, USA, 8Bioinformatics Center, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200 Copenhagen N, Denmark, 9Molecular Phylogenetics, Department of Biology, TU Kaiserslautern, 67653 Kaiserslautern, Germany, 10EMBL Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany, & Institute of Informatics, University of Warsaw, Poland, and 11RIKEN OmicsScience Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa-ken, 230-0045, Japan

*To whom correspondence should be addressed. Dr. Peter Cock, E-mail: peter.cock{at}scri.ac.uk, p.j.a.cock{at}googlemail.com


  Abstract

Summary: The Biopython project is a mature open source international collaboration of volunteer developers, providing Python libraries for a wide range of bioinformatics problems. Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macromolecular structures, interacting with common tools such as BLAST, ClustalW, and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.

Availability: Biopython is freely available, with documentation and source code, at http://www.biopython.org under the Biopython license.

Contact: All queries should be directed to the Biopython mailing lists, see http://www.biopython.org/wiki/Mailing_lists.

Associate Editor: Prof. Dmitrij Frishman

Received on March 11, 2009; revised on March 11, 2009; accepted on March 16, 2009

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