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      Is Open Access

      The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell

      research-article
      Author(s): 1 , 2 , * , 1 , 2 , 3
      Publication date (Electronic):
      Journal: Bioinformatics
      Publisher: Oxford University Press

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          Abstract

          Summary: We present a suite of U nix shell programs for processing any number of phylogenetic trees of any size. They perform frequently-used tree operations without requiring user interaction. They also allow tree drawing as scalable vector graphics (SVG), suitable for high-quality presentations and further editing, and as ASCII graphics for command-line inspection. As an example we include an implementation of bootscanning, a procedure for finding recombination breakpoints in viral genomes.

          Availability: C source code, Python bindings and executables for various platforms are available from http://cegg.unige.ch/newick_utils. The distribution includes a manual and example data. The package is distributed under the BSD License.

          Contact: thomas.junier@ 123456unige.ch

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          The Bioperl toolkit: Perl modules for the life sciences.

          Jason E Stajich, David Block, Kris Boulez … (2002)
          The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
          Article 0 comments Cited 727 times – based on 0 reviews     Review now
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            R: a language and environment for statistic computing

            R.D.C. Team, R Development Core Team, RDC Team … (2008)
            Article 0 comments Cited 395 times – based on 0 reviews     Review now
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              Identification of breakpoints in intergenotypic recombinants of HIV type 1 by bootscanning.

              M O Salminen, J Carr, D Burke … (1995)
              Article 0 comments Cited 252 times – based on 0 reviews     Review now
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 1 July 2010
                Publication date (Electronic): 13 May 2010
                Publication date PMC-release: 13 May 2010
                Volume: 26
                Issue: 13
                Pages: 1669-1670
                Affiliations
                1 Department of Genetic Medicine and Development, University of Geneva Medical School, 2 Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 3 Imperial College London, South Kensington Campus, SW7 2AZ, London, UK
                Author notes
                * To whom correspondence should be addressed.

                Associate Editor: Alex Bateman

                Article
                Publisher ID: btq243
                DOI: 10.1093/bioinformatics/btq243
                PMC ID: 2887050
                PubMed ID: 20472542
                SO-VID: 4d673183-1f93-4edf-990b-2e694ac7b826
                Copyright © © The Author(s) 2010. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 3 March 2010
                Date revision received : 27 April 2010
                Date accepted : 29 April 2010
                Categories
                Subject: Applications Note
                Subject: Phylogenetics

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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