Here's my PAUP block:
Lset base=equal nst=6 rmat=(1.9080 1.9080 1.9080 1.0000 3.4929) rates=gamma shape=0.7030 ncat=4 pinvar=0;
Any help would be appreciated. Please DO NOT tell me to read the MrBayes manual - I did and it did not help at all.
Caner Aktas
As far as I know, some PAUP commands are not compatible with MrBayes. Consider using MrModeltest:
https://github.com/nylander/MrModeltest2
This discussion may also be helpful:
https://groups.google.com/forum/#!topic/jmodeltest/66XZpjKpvxA
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