What's new in NINJA 1.2.1
Jun 17, 2013
- Handle case where two sequences in an alignment share no columns in common. Assigns maximum distance to such pairs of sequences.
New in NINJA 1.2.0 (Jun 17, 2013)
- 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"
New in NINJA 1.0.4 (Jun 17, 2013)
- 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
New in NINJA 1.0.3 (Jun 17, 2013)
- Cleaned up baffling organization of contents, especially for source code.
New in NINJA 1.0.2 (Jun 17, 2013)
- Improved documentation.
- Implemented new default method.
- Minor I/O bug fixes.
- Completed integration with Mesquite.