[Mesquitelist] Announcing new neighbor-joining package (NINJA)

[David Maddison]

As a follow-up to Travis's note about NINJA:  in bringing NINJA to Mesquite, Travis and I realized that NINJA's speed was not matched by a similarly fast distance calculator in Mesquite.  That is, while NINJA is very fast, Mesquite's distance calculations aren't.  

While I have improved the distance calculations by about 2x for the yet-to-be-released version 2.73 of Mesquite, they are still relatively slow.  We will work on that in the future.  Also, models for calculating distances do not include the full set available in other programs.  For example, Mesquite can calculate F84 distances (similar to HKY85), but cannot yet calculate distances using a GTR model.  Those, too, we hope to improve.  In the meantime, NINJA now brings a fast NJ calculator for the distance measures Mesquite does support.

[BTW, once NINJA is installed, you can calculate a neighbor-joining tree using Taxa&Trees > Tree Inference > Neighbor-Joining (NINJA).]

David


---------------------------------
David R. Maddison
Department of Zoology
3029 Cordley Hall
Oregon State University
Corvallis, OR  97331   USA

david.maddison at science.oregonstate.edu

http://david.bembidion.org
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