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Yes. Image Plus will handle FITS and calibration files.
So does DeepSkyStacker...however, if you need to scale the dark frames, DSS has problems. It assumes that the dark frames are the same exposure as the lights. If you've got a 30min dark frame and need to scale it to match a 10min light frame - it will not work. CCDStack, MaximDL, Image Plus and others support dark frame scaling.
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