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Bioinformatics. 2010 Jul 1;26(13):1669-70. doi: 10.1093/bioinformatics/btq243. Epub 2010 May 13.

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

Author information

1
Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland. thomas.junier@unige.ch

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

PMID:
20472542
PMCID:
PMC2887050
DOI:
10.1093/bioinformatics/btq243
[Indexed for MEDLINE]
Free PMC Article

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