Paup informative sites?

Mark Siddall mes at zoo.toronto.edu
Fri Nov 24 10:39:22 EST 1995


In article <491hac$ef6 at montespan.pasteur.fr> Hassan Badrane <hbadrane at pasteur.fr> writes:
>Hello,
>Another programme can count the variable sites, the informatives sites etc...
>in a given alignement. it's MEGA which run on PCs.
>

I have written a very simple program which, unlike MEGA, is free and is ftpable 
from zoo.toronto.edu/pub called "tease.exe"

It will strip out all uninformative characters from an data set of anysize.
One ceveat is that your data need to be in Hennig86 format.
That is: A=0, C=1, G=2, T=3, - = ? or -.
And the data must be arranged as follows:
xread
1200 5
one 0113201232 ... <base 1200>
two 0113201232 ... <base 1200>
thr 0113201232 ... <base 1200>
fou 0113201232 ... <base 1200>
fiv 0113201232 ... <base 1200>

If you have PAUP, you can simply take your file and export for Hennig86.

The application is for DOS.


It works much faster at removing uninformative than MacClade does for 
example.

It only removes characters that are uninformative under ALL optimization 
criteria, tells you which characters were removed and creates a new file
with the informative characters only.

Mark
-- 
Mark E. Siddall                "I don't mind a parasite...
mes at vims.edu                    I object to a cut-rate one" 
Virginia Inst. Marine Sci.                     - Rick
Gloucester Point, VA, 23062



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