Dear Mark,

In HyPhy branches are identified with the node they END in (otherwise you can't uniquely resolve branch-node mapping for internal nodes with multiple children). For example, in the tree ...((a,b)Node1,c)Node2),... specify Node1 to examine the parent lineage of (a,b) and Node2 - to examine the parent lineage of ((a,b),c).

HTH,
Sergei