PHYLIP

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 
http://www.t10.lanl.gov/billb/weighbor

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version of weighbor is out of date (if someone can compile for Mac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...

Bill

------------------------------------
William J. Bruno, Ph.D.
DNA Mining Informatics Software, LLC
http://dnaMining.com

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