The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
- PMID: 20472542
- PMCID: PMC2887050
- DOI: 10.1093/bioinformatics/btq243
The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
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: thomas.junier@unige.ch
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