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tjunier edited this page Dec 11, 2012 · 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

2012-12-05 - changed de-rooting algorithm so it can deal with the root's children each having two children of their own.

2012-11-15 - fixed bug in rooting when clade labels are support values

2012-08-01 - NOTE I will have to slow down the work on this project, as I do it all in my free time and this resource is really scarce now :-| I do not plan to give up , though.

2012-06-21 - Will try to port the manual to ConTeXt. This may solve some problems I have now with LaTeX. Clickable ToC seems to work, and the build process will be simpler.

2012-05-29

Feature freeze for release 1.7. This includes:

  • Using CMake as a build system
  • Display trees with VT100-style pseudo-graphical characters

2011-12-15

nw_display can draw trees at a fixed scale (rather than only a fixed width, as before).

2011-11-23

Stable Release 1.6 is out. You can get it from here with Git, or get tarballs (including binaries) from http://cegg.unige.ch/newick_utils. New in this release:

  • a new version of nw_ed that embeds a Lua interpreter
  • nw_reroot can do longest-branch rerooting

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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