Greetings Fellow Netters:
Im hoping that someone can help me out with a few questions I have
about Nucleotide Divergence among populations (not nucleotide diversity).
I am currently analyzing some restriction-sites data (among populations)
using the REAP program of McElroy et al. (1992).
Everything was going fine, UNTIL I obtained some negative values for
nucleotide divergence among populations. I think these negative values
are affecting the resulting dendrograms (i.e., they are not an intuitive
represtatiom of the data). Has anyone out there used this program?
Does anyone know what effect these negative values have on clustering
algorithms (Ive been using UPGMA in the Neighbor program of PHYLIP)?
What causes a negative nucleotide divergence estimate? Is there a
better way of examining population relatedness with this type of data,
or a better program?
If you can help me out please e-mail me at the address below.
Thanks in advance.
JimF at fishgame.state.ak.us