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I am looking for a solution in which I can add watermark to the given video at given frame.

Is there any utility/tool to do so ?

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mencoder can definitely do it, although the folks I know tend to use one of the free Windows apps (so I'm guessing you could run one of them under Wine)

Also bmovl should be able to do it. Check out this thread.

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If you want to do this programatically mencoder is the tool for the job. You'll need a static image (or generate one programatialy with ImageMagic, gd, etc) and some time to play with filters.

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