Announcing Weighted NJ (Weighbor) Program

Bill Bruno billb at
Fri Jan 28 20:16:05 EST 2000

Weighbor 1.0.1 has been released.  Download it for free at or ftp at  Source code (in C) is provided,
and we encourage you to help us post an executable for your machine if
you can make one.

Weighbor uses a likelihood function on the distances to compute a tree
from a distance matrix.  A number of heuristics, including neighbor
joining-like iterated clustering are used to make the program much
faster than full likelihood-based methods such as fastDNAml.  I've
run it on 250 sequences in 20 minutes on a workstation.

When using weighbor, the local tree structure is much less sensitive
to "noise" coming from distant taxa, compared to regular neighbor-joining. 
The method and its performance are described in:

William J. Bruno, Nicholas D. Socci, and Aaron L. Halpern, "Weighted
Neighbor Joining: A Likelihood-Based Approach to Distance-Based
Phylogeny Reconstruction." Mol. Biol. Evol.  17 (1): 189-197 (2000).

Enjoy, and let us know if you have comments or questions.

billb at


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