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PAUP and 3rd pos TS's question

Niklas Wikström wikstrom at botan.su.se
Mon Jan 13 07:46:44 EST 1997


In article <32D6CC73.481F at aurora.alaska.edu>, John Demboski
<ftjrd at aurora.alaska.edu> wrote:

> 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.
> 


Here is what you have to do

1:st you number the codon positions over the sequences like this

     CODPOSSET UNTITLED = 
      1: 1-727\3, 
      2: 2-728\3, 
      3: 3-726\3;

this is an example with 728 basepair sequences

2:nd you define a stepmatrix where transitions are coded as zero steps but
transversions are coded as one and give it a name (e.g. ttbias01) like
below.

After that you create a typeset and assign that character type to all the
third positions.

   BEGIN ASSUMPTIONS;


   USERTYPE ttbias01 STEPMATRIX = 4
        A C G T
    [A] . 1 0 1
    [C] 1 . 1 0
    [G] 0 1 . 1
    [T] 1 0 1 .
   ;
   OPTIONS  DEFTYPE=unord PolyTcount=MINSTEPS ;

   TYPESET * UNTITLED  = ttbias21: 3-726\3;

   ENDBLOCK;



I hope this will help you.

-- 
Niklas Wikström
Dept. of Botany
Stockholm university
S-10691 Stockholm
SWEDEN
e.mail: wikstrom at botan.su.se



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