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