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
