Click Ctrl + Shift and drag over the nodes to select them. With the nodes selected, use the icons on the main toolbar to make a function, group or section:
Make function Complicated chains of nodes can be dismembered and merged into single functions. These functions can be used to simplify the analysis structure or to save / duplicate separated parts of an analysis for another use. After clicking this button a new function named Function is created and the selected nodes are hidden inside as its inner nodes. To decompose a function, reveal the context menu over the function and select 
Decompose function. All inner nodes of the function will be restored to their original positions.
To edit a function, select 
Edit Function from the context menu. GA3 editor is switched to the function editing mode showing only the inner nodes of the edited function. The top input parameters are substituted with inputs of the function. It is possible to change the inner node settings or the structure of the graph inside the function. All changes are reflected in the function inputs and outputs. Use the 
button to end the editing mode.
Click on 
Build Function GUI in the context menu over a function. Then check which inner nodes will be visible in the parameters window of the function being set.
Make group Aggregates nodes below each other within a single group node. To decompose the group click 
Decompose group in the context menu.
Make section Creates a section (color rectangle) which can be further sized by pulling the bottom right rectangle. More nodes can be added to the section by dragging and dropping.
Duplicate Duplicates the selected function, group or section.
Delete Deletes the selected function, group or section.