The Newick Utilities are a set of Unix shell tools for high-throughput processing of phylogenetic trees.
They accept trees of any size and can process any number of trees in a single run. The perform functions such as:
They are written in C and distributed under the BSD License.
2014-04 - new version of the manual, rewritten in ConTeXt (previously in LaTeX).
This Github repository is mainly for users who want the latest, bleeding-edge (and therefore less stable) version. For the stable version (which also has binaries), the official site is http://cegg.unige.ch/newick_utils (though the stable release is also available here, as branch "stable").
If you use the Newick Utilities in published work, please cite:
The Newick Utilities: High-throughput Phylogenetic tree Processing in the UNIX Shell
Thomas Junier and Evgeny M. Zdobnov
Bioinformatics 2010 26:1669-1670