Thank you and I did try this but it did not work.

I tried it at the end with the begin paup;  end; commend and without it.

I tried the following 

begin paup;

pscores /tl ci ri rc;

end;

ALSO

INDEX = RC|CI|RI;

any other suggestions

I was told for cipres

Anything you can put in a PAUP block of your Nexus file should work fine. It is full PAUP, but we didn't try to implement a full interface to configure everything

I think I am missing something and would really like this to work.

Hi,

You should maybe check that trees of interest are still in memory. Also, did you try to run the command directly in PAUP after the tree search, just to check if the error is in the nexus formating or from PAUP.

I join an old ammonite nexus file that works on my computer. Try it.

Best, Jérémie