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Announcing Weighted NJ (Weighbor) Program

Bill Bruno billb at t10.lanl.gov
Fri Jan 28 20:16:05 EST 2000

Weighbor 1.0.1 has been released.  Download it for free at
www.t10.lanl.gov/billb/weighbor or ftp at
ftp-t10.lanl.gov/pub/billb/weighbor.  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 lanl.gov


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