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Our asphalt shingles have extensive roof algae on them, may a metal roof be installed directly over the asphalt roof?
From a standpoint of installing over biological growth, underlayment will be installed over it which will isolate it from light and moisture so it will die. As far as whether the unevenness of any biological growth will cause problems with the new roof, probably not -- but a lot depends upon how forgiving the new roof panels are.
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