Howdy folks,
can anyone help me out? Maybe this has been addressed before. I have
a common situation with my mtDNA (cyt b) data set. Saturation analyses
has revealed that 3rd position transistions are saturated above the
subgeneric level. I would like to be able to analyze these data without
dropping out ALL 3rd position changes (transversions are not
saturated). Is there a commmand(s) that i can include in my PAUP NEXUS
file to remove only these 3rd position transistions? If this is
possible, is it accomplished by an "exclude", "ignore" or weighting
commmand?
Can a step-matrix of some sort be setup to address this?
I notice that in many papers, in the case of saturation, all 3rd
positions are dropped from analyses. I would like to avoid that if at
all possible.
Please respond to me directly as I am not able to access this newsgroup
on a regular basis.
Cheers!
John Demboski
ftjrd at aurora.alaska.edu
University of Alaska Fairbanks
