Graphviz

Graphviz is open source graph visualization software. It has several main graph layout programs.

15 Alternatives To Graphviz

Code2Flow

An easy solution to create product flows.

Dia

Dia is a GTK+ based diagram creation program for GNU/Linux, MacOS X, Unix, and Windows, and is released under the GPL license.
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Gephi

Gephi is an open-source software for visualizing and analyzing large networks graphs.
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LucidChart

LucidChart is the missing link in online productivity suites. LucidChart allows users to create, collaborate on, and publish attractive flowcharts and other diagrams from a web browser.

Netglub

Netglub, the really open source information gathering solution.

PlantUML

PlantUML is an open-source tool that uses simple textual descriptions to draw UML diagrams.

Poortego

Open-source python project to handle the storage and linking of open-source intelligence (ala Maltego) - mgeide/poortego
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StarUML

StarUML

Trumpet

Postcards to the President
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UMLet

UMLet - Free UML Tool for Fast UML Diagrams
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Visio

Simplify and communicate complex information using data-linked diagrams.

dradis

Dradis is the open-source reporting and collaboration tool for IT security professionals.

xfig

Xfig is a free and open source vector graphics editor which runs under the X Window System on most…
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yEd Graph Editor

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.