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version of weighbor is out of date (if someone can compile for Mac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