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Visual Understanding Environment - Visual Understanding Environment (VUE) is a mind-mapping and concept-mapping tool.
Freeplane - Freeplane is a powerful and free software for building mind maps.
Protégé - Protégé is a free, open source ontology editor and knowledge-base framework.
Linked Ideas - A macOS/iOS apps to treat ideas as links of concepts.
Xmind - Xmind is a brainstorming and mind mapping application.
vym - VYM (View Your Mind) is a tool to generate and manipulate maps which show your thoughts.