Dear Ulf,
There are two ways to inspect trees or specify subtrees a priori:
(1). Edit the tree string to give an internal node you need to label a custom name. For example, if you want to refer to the subtree ((1,2),3) in the following tree: (((1,2),3),(4,5),6), you can explicitly edit the tree string as such: (((1,2),3)MySubtree,(4,5),6). Naturally, you can call 'MySubtree' anything you want, but in the subtreeselectioncomparison analysis dialog, you will be able to see 'MySubtree' as a choice.
(2). I have edited the subtreeselectioncomparison.bf analysis so that it now displays a graphic of the tree with all the nodes labeled behind the selection dialog. You can move the selection dialog to the side and inspect the tree for the name of the subtree-rooting internal node you wish to use. This only works on Mac and Windows. The modified analysis will be included in today's and later HyPhy builds. You can also download it directly Multimedia File Viewing and Clickable Links are available for Registered Members only!! You need to
and replace the corresponding file in 'TemplateBatchFiles'.
Hope this helps and thanks for your feedback!
Sergei