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flowchart.fun - An open-source tool for generating flowcharts from text
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.
draw.io - Online diagramming application
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
yEd - yEd is a free desktop application to quickly create, import, edit, and automatically arrange diagrams. It runs on Windows, Mac OS X, and Unix/Linux.
Freeplane - Freeplane is a powerful and free software for building mind maps.