Try the Materials Informatics Toolkit, which is designed to easily handle SMILES data. This and other helpful add-ins are available in the JMP® Marketplace
The idea: The user selects some data points and for each branch of the tree, the %fraction gets highlighted - similar to the %filling of the Histogram Plot (bottom left)
Very interesting! That would be a nice feature. I don't think that's possible currently. Unless someone else chimes in with a solution, this might be a good candidate for the JMP Wish List.