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What is the best online application (Java or Javascript) or basic application (Win) to visualizing website relationship in graphic?

Application should draw lines between website pages starting from given address.

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If you mean visitors flow report (aka. page transitions report):

Google Analytics (closed-source + free) (more info):

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Piwik (open-source + free):

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You might also be interested in looking for Sankey diagrams, e.g. using D3.js (open-source + free): http://bost.ocks.org/mike/sankey/

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