Dear Sergei I am triying to make a dNdSRateAnalysis.bf but with rooted trees thus setting ACCEPT_ROOTED_TREES=1

but if i do this i get trees with unusual brach lengths (e.g. 1700). If do not use the rooted trees option I do not know what happens with the root when afterwards I use meanpath.bf to compute paths to the "entire root of the tree", if this root the same root I had with the original input tree?.
thanks,
Antonio