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

Dear Antonio,

wrote on Dec 19^th, 2005 at 4:36am:

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?.

Long branch lengths are surely odd. dNdSRateAnalysis.bf models can not use the information about the root (as they are all time-reversible). I would suggest running dNdSRateAnalysis.bf with an unrooted tree, then rooting it (e.g. in the tree viewer panel) on the branch you want to be the root, and then using meanpath.bf.

HTH,
Sergei