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Bill Bruno wjb at dnamining.com
Thu Mar 29 04:58:21 EST 2001

> Bad idea. Use NEIGHBOR instead. A lot better, and a lot faster. 

I disagree.  Neighbor is a lot faster, but in my tests fitch
is more robust if you have long branches.  
My (admittedly biased) opinion is that the best choice
is weighbor, available free from 

For test results see
              W. J. B., N. D. Socci, & A. L. Halpern, "Weighted
              Neighbor Joining: A Likelihood-Based Approach to
              Distance-Based Phylogeny Reconstruction," Mol. Biol.
              Evol. 17 189-197 (2000).

If you don't get the journal, see http://www.t10.lanl.gov/billb/weighbor/paper/

Weighbor can be used with PHYLIP to do bootstraps; note the Mac
version of weighbor is out of date (if someone can compile for Mac
I'd appreciate it).

I'm not sure I agree with using bootstrapping to find the best
tree either...


William J. Bruno, Ph.D.
DNA Mining Informatics Software, LLC


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