Use a state machine with shift registers (you can use a cluster to bundle related data together) and pass that through the state machine. You can create more descrete states to simply your decision points and only need to make simple comparisons within those states. You named several potential states in your reply: denature, anneal and extend for example. Map out your state tasks and the transitions that require you to switch from one state to the next. You may find that you are trying to do too much stuff in one case now.
As for global variables use queues, notifiers or action engines to pass data between subVI. Any of these help to decouple your subVIs from each other. The use of globals tightly couples your code and makes any type of reuse very difficult.
Mark Yedinak
Certified LabVIEW Architect
LabVIEW Champion
"Does anyone know where the love of God goes when the waves turn the minutes to hours?"
Wreck of the Edmund Fitzgerald - Gordon Lightfoot
