Default setting of PNJ is the automatic modus as described above. In contrast to the automatic modus you can interact in the alternative modi either in the fist step (half automatic) or after every iteration (half automatic, every step). Both modi are manual as well as automatic in that profiles are set by the user and by the algorithm. However, in the manual modi of PNJ, only exclusively the user is enabled to agglomerate sequences to profiles.
Generally you have to interact after the first tree with bootstrap values has been calculated. The treeviewer opens automatically and at each node you will find the node number and the associated bootstrap values. After minimizing the treeviewer window you can specify the subtree in that you write the number of the corresponding node into a small popped up window. E.g. if you would like build profile of nodes 3,4,17 you have to write: 3/4/17, 3,4,17, or 3;4;17. After pressing the OK button the next iteration of PNJ is started.