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


BACKGROUND
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.


BACKGROUND
thomas.junier@unige.ch
Junier
Thomas
T
Department of Genetic Medicine and Development, University of Geneva Medical School, 1 rue Michel-Servet, 1211 Geneva, Switzerland. thomas.junier@unige.ch
Zdobnov
Evgeny M
EM
D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D016013:Likelihood Functions; D010802:Phylogeny; D011381:Programming Languages; D016415:Sequence Alignment; D012984:Software
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