The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell

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 The distribution includes a manual and example data. The package is distributed under the BSD License.

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