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[Walter Boeger]

Hi all,

I am sure a lot of you, that deal with PAUP* (and other computer phylogeny software), already ran into this same question.  How to distinguish between really "missing" and just "does not apply" characters?   Was anyone sucessful in doing that???  I have tried to use a distinct code (say, a "x") for these "does not apply" states and built a usertype stepmatrix to indicate that the "cost" of going from any other state to "x" would be "0" (hoping that this means "do not consider the "x" " for the software), but was not successfull since PAUP did not accept the stepmatrix below:

begin assumptions;
 usertype unav (stepmatrix)=6 01234x

 - 1 2 3 4 0
 1 - 1 2 3 0
 2 1 - 1 2 0
 3 2 1 - 1 0
 4 3 2 1 - 0
 0 0 0 0 0 -;



Well....I would reaaaallly appreciate if anyone of you has some suggestion on how to handle with this problem...

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Walter A. Boeger, Ph.D.
Dept Zoologia, UFPR
Caixa Postal 19073
Curitiba, PR 81531-990
Brasil
phone: 55413663144 ext. 206
fax: 55412662042
wboeger at bio.ufpr.br
http://zoo.bio.ufpr.br/departamento
ICQ:  36546488
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So many worms...so little time
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