Sergei,

I am trying to run SubtreeSelectionComparison.bf and specify an internal node as the 'subtree'.  I've run into a behavior in HYPHY that I can't understand or work-around.  Consider the following tree:

( ib,  ((((ch,dm),(sr,hw)),ht),er) , ((bu,((me,(hl,is)),do)),ao) );

I want to specify the subtree ((((ch,dm),(sr,hw)),ht),er) as the focal clade. in SSC.bf

When I open the treefile directly in HYPHY using 'open tree' it seems to read it correctly as an unrooted tree (left of figure).  But when opened via the SSC.bf it forces a very unhelpful rooting/ordering of taxa (right of figure) making it impossible to specify my desired subtree.  

Why is it forcing this weird rooting and what can I do to make it read the file in a more useful way?  Am I doing something wrong with the input somehow?

Thanks, Jamie

problem_trees.png

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I suspect the DO_TREE_REBALANCE flag is the culprit.
It is being set to 0 prior to calling the qndhelper1.ibf script, but in that script it is set back to 1.

Cheers,
- Art.

Yes, that does seem to make all the difference.  Thank you very much!

Jamie