Work

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

Year: 2010

Type: article

Abstract: 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: [email protected]

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btq243

Authors: Thomas Junier, Evgeny M. Zdobnov

Institutions: University of Geneva, SIB Swiss Institute of Bioinformatics, Imperial College London

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: hybrid

Estimated APC paid: $3,989

Funders: National Science Foundation, Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung