NINJA is software for inferring large-scale neighbor-joining phylogenies.

According to benchmark tests, at the time of release, NINJA is the fastest available tool for computing correct neighbor-joining phylogenies for inputs of more than 10,000 sequences. It is more than 10x faster than the fastest implementation of the canonical neighbor-joining algorithm (QuickTree). Details of the software are available in a paper appearing at WABI 2009 (see link below).

URL of this page		http://nimbletwist.com/software/ninja
Terms of Use		LGPL
Distribution		Ninja.jar (you may need to right-click, then choose "save link as")
Citation		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. (LNCS webpage,preprint)
Contact		Travis Wheeler travis _ at _ nimbletwist.com