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I'm not to sure but you could replace all the roofing with new shingles dark enough to disguise the staining, or with shingles laced with copper granules, which are lethal to algae. But that would only make sense if the shingles were worn out. To keep the algae from coming back, insert 6-inch-wide strips of zinc or copper under the row of shingling closest to the roof peak, leaving an inch or two of the lower edge exposed to the weather.

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Q: How do you kill algae in shower and on roof shingles?
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