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Dia - Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
asciiflow - Infinite ASCII diagrams, save to Google Drive, resize, freeform draw, and export straight to text/html.
Graphity - Graphity is a diagram editor that can be used to quickly and effectively generate drawings and to...
Core2D - A multi-platform data driven 2D diagram editor.
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.
PathVisio - Open-source and free pathway analysis and pathway drawing software. Allows drawing, editing and analysis of biological pathways.