Alt click on a node connection automatically disconnect it from the other nodes. And there is some nodes which can be easily summoned by pressing a key and clicking at the same time. Like B+click will place a branch, and S+click a sequence.
If you're willing to compile it, Aseprite is a great option as well.
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Nintendo UK uploaded a bunch of paper scans, which show the way the cult game levels were planned.
With modern game development, everything is going digital. Like every office, game developers tend to type, not to write, they tend to use Wacom instead of the pencil. Yet, back in the day, everything was analog. Developers from Nintendo used just simple drawings to make their amazing masterpieces.
Nintendo UK shared some scans, which show the way the Legend of Zelda game levels were planned. You can find Takashi Tezuka’s skull room drawing, with a comparison to how it appeared in game. There are drawings by Shigeru Miyamoto and other developers as well.
Check out this video to see every part of the game drawn by hand. Pretty amazing stuff.