I am wondering is there any tool which can help visualize relations between tasks/bugs, I mean dependencies like related to/blocks/clone/etc.
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There is the Links Hierarchy plugin, though I'm not sure if that supports JIRA 4.4. There is also the REST example at https://developer.atlassian.com/display/JIRADEV/JIRA+REST+API+Version+2+Tutorial#JIRARESTAPIVersion2Tutorial-Example%231%3AGraphingImageLinks

mdoar
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the linking to the draw-chart.py on that page is broken. Here is the source code: https://developer.atlassian.com/download/attachments/4227078/draw-chart.py?version=2&modificationDate=1285030688582 – hansaplast Mar 15 '13 at 09:47
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Vivid Trace visualizes relations between tasks/bugs for any/all of the issue link types you mention, and it can graph a given issue, component, version, or even a whole project. https://vivid-inc.net/
(Disclaimer: We make it.)

Vivid Inc.
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@JohnHunt Nothing to announce at this time, but I'd be happy to keep you informed! – Vivid Inc. Sep 09 '17 at 08:35