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The NINJA Mesquite package requires Mesquite 2.72 or later.

To install the NINJA package of modules

  • start up Mesquite
  • use the "Check Now for Notices/Installs" menu item in the File Menu
  • enter the URL http://mesquiteproject.org/packages/NINJA/install.xml
Mesquite will then present a dialog box with information, and from which you can install NINJA.

Once NINJA is installed, you can calculate a neighbor-joining tree using the menus: Taxa&Trees > Tree Inference > Neighbor-Joining (NINJA).

If you use NINJA from within Mesquite, please cite the paper that describes NINJA:
Wheeler, T.J. 2009. Large-scale neighbor-joining with NINJA. In S.L. Salzberg and T. Warnow (Eds.), Proceedings of the 9th Workshop on Algorithms in Bioinformatics. WABI 2009, pp. 375-389. Springer, Berlin.