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Thomas Junier edited this page Jun 2, 2014 · 20 revisions

The Newick Utilities

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:

  • (re)-rooting
  • extracting branch length
  • displaying (ASCII graphics or SVG)
  • extracting subtrees
  • renaming nodes
  • etc.

They are written in C and distributed under the BSD License.

New

2014-04 - new version of the manual, rewritten in ConTeXt (previously in LaTeX).

Older News

Main site

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").

Publication

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
http://bioinformatics.oxfordjournals.org/content/26/13/1669.full
doi:10.1093/bioinformatics/btq243

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