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 http: //cegg. unige. ch/newickᵤtils. The distribution includes a manual and example data. The package is distributed under the BSD License. CONTACT: thomas. junier@unige. ch