PAUP and 3rd pos TS's question

John Demboski ftjrd at aurora.alaska.edu
Fri Jan 10 18:10:47 EST 1997


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



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