Download ninja zip file :
You must have Java version ≥ 5
Read the documentation page for further instructions.
You may also download a preprint of the 2009 WABI paper.
- 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)
- Handle case where two sequences in an alignment share no columns in
common. Assigns maximum distance to such pairs of sequences.
- 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
- 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"
- 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
Cleaned up baffling organization of contents, especially for source code.
Improved documentation. Implemented new default method. Minor I/O bug fixes.
Completed integration with Mesquite.