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Download ninja zip file :   ninja.tgz

You must have Java version ≥ 5 (aka v1.5). Read the documentation page for further instructions.

You may also download a preprint of the 2009 WABI paper.

Version History

Current Version

ninja_1.2.2.tgz (08/31/2013)

  • Minor changes to the ./ninja script to (a) enable a new --mem flag, and (b) enable the script to identify the location of the ./ninja function even when it is called form else where and is symlinked.

Previous Versions (placed here for the sake of posterity; no reason to use them)

ninja_1.2.1.tgz (11/17/10)

  • Handle case where two sequences in an alignment share no columns in common. Assigns maximum distance to such pairs of sequences.

ninja_1.2.0.tgz (11/09/10)

  • Primary change is addition of distance computation. NINJA is now able to compute distances for alignments without requiring use of other tools.
  • Improved shell script to allow it to be called from other directories
  • Fixed bug in which distances were occasionally incorrectly read by the internal-memory variant (I don't believe this could have affected results from quicktree-derived distance files, but FastTree-derived files occasionally found this NINJA bug)
  • Fixed bug in which the branch lengths were incorrect for the branches involved in the final merge
  • Fixed bug in which a flawed correction was being applied to negative branch lengths in the external-memory variant
  • Changed the names of methods from "binheap"/"candheap" to the more descriptive (I hope) "inmem"/"extmem"

ninja_1.0.4.tgz (10/11/10)

  • Added a --out flag to print output somewhere besides stdout
  • Added a shell script that runs Ninja.jar with appropriate Java flags
  • Bundled in a .tgz file
  • Fixed bug in which two lines of debugging code were being written to the tree file

Ninja.1.0.3.jar (02/22/10)
Cleaned up baffling organization of contents, especially for source code.

Ninja.1.0.2.jar (01/25/10)
Improved documentation. Implemented new default method. Minor I/O bug fixes. Completed integration with Mesquite.

Ninja.1.0.0.jar (09/10/09)
Initial release.