Yes it can be done in GIMP.
Open your image in GIMP. Choose a new background colour which is as close to the
background your image is going to be displayed over. In GIMP click Filters > Web
> Semi flatten. Repeat for each layer of your animation. Now save your GIF. Now
see how it looks when displayed over the background.
bktheman34 (via www.gimpusers.com/forums)
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