you still get the warning because model parameters and br-lens of the
final tree will still be estimated under GAMMA, this is nothing to worry
about, since a high alpha parameter does not mean that you should not
use Gamma, but rather that you don't need to use GAMMA which will make
the likelihood computations during the tree search execute faster,
alexis
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org