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tjunier edited this page Nov 16, 2011 · 20 revisions

The Newick Utilities

The Newick Utilities are a set of Unix shell tools for processing 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.

News

2011-09-23
The latest stable release is almost done. It includes a new version of nw_ed that embeds a Lua interpreter, as well as simpler, faster (well, hopefully) memory management. Trees can now be rerooted on the longest branch, in case the outgroup is not known/present/etc.

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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