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

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      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 macro molecular 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 www.biopython.org under the Biopython license.Contact: All queries should be directed to the Biopython mailing lists, see www.biopython.org/wiki/_Mailing_listspeter.cock@scri.ac.uk.

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      Most cited references 22

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      CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

      The sensitivity of the commonly used progressive multiple sequence alignment method has been greatly improved for the alignment of divergent protein sequences. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. These modifications are incorporated into a new program, CLUSTAL W which is freely available.
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        genepop'007: a complete re-implementation of the genepop software for Windows and Linux.

        This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls. © 2007 The Author.
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          EMBOSS: the European Molecular Biology Open Software Suite.

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            Author and article information

            Affiliations
            1Plant Pathology, SCRI, Invergowrie, Dundee, DD2 5DA, 2Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK, 3Institute for Genome Sciences and Policy, Duke University Medical Center, Durham, NC, 4Department of Molecular Biology, Simches Research Center, Massachusetts General Hospital, 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, UK, 10EMBL Heidelberg, Meyerhofstraβe 1, 69117 Heidelberg, Germany, 11Institute of Informatics, University of Warsaw, Poland and 12RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama-shi, Kanagawa-ken, 230-0045, Japan
            Author notes
            *To whom correspondence should be addressed.

            Associate Editor: Dmitrij Frishman

            Journal
            Bioinformatics
            bioinformatics
            bioinfo
            Bioinformatics
            Oxford University Press
            1367-4803
            1460-2059
            1 June 2009
            20 March 2009
            20 March 2009
            : 25
            : 11
            : 1422-1423
            2682512
            19304878
            10.1093/bioinformatics/btp163
            btp163
            © 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.

            Categories
            Applications Note
            Sequence Analysis

            Bioinformatics & Computational biology

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