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Jira - The #1 software development tool used by agile teams. Jira Software is built for every member of your software team to plan, track, and release great software.
Xmind - Xmind is a brainstorming and mind mapping application.
Redmine - Flexible project management web application
MindMeister - Create, share and collaboratively work on mind maps with MindMeister, the leading online mind mapping software. Includes apps for iPhone, iPad and Android.
Trac - Trac is a project management and bug/issue tracking system. Provides an interface to Subversion and an integrated wiki.
Coggle - Coggle is a simple, beautiful, powerful way of structuring information.