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

Fig. 1.

Bootscanning using PhyML, EMBOSS, Muscle, Newick utilities, GNUPlot and standard Unix shell programs. The species with the lowest distance is the reference's nearest neighbor (by distance along tree branches). A recombination breakpoint is predicted near position 450, as the nearest neighbor changes abruptly.

Fig. 2.

Average run times (10 samples) of rerooting tasks on various tree sizes in different implementations. The task involved reading, rerooting and printing out the tree as Newick. Runs of the BioPerl and APE implementation on the 20 000-leaf tree did not complete. Error bars show 1 SD. Computer: 3 GHz 64 bit Intel Core 2 Duo, 1 GB RAM, Linux 2.6. Made with R (R Development Core Team, 2008).