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

Junier, Thomas ; Zdobnov, Evgeny M.

In: Bioinformatics, 2010, vol. 26, no. 13, p. 1669-1670

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    Titre
    • The Newick utilities: high-throughput phylogenetic tree processing in the Unix shell
    Auteur
    • Junier, Thomas. Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and Imperial College London, South Kensington Campus, SW7 2AZ, London, UK
    • Zdobnov, Evgeny M.. Department of Genetic Medicine and Development, University of Geneva Medical School, Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and Imperial College London, South Kensington Campus, SW7 2AZ, London, UK
    Type de document
    • Postprint
    Identifiant OAI-PMH
    • oai:doc.rero.ch:304329
    Summary
    Summary: We present a suite of Unix 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@unige.ch