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Look at the instructions for Form 2210. They address the situation. It's been awhile, but I believe you calculate tax for both as if they had filed separately & then allocate 2006 tax liability to each based on the ratio of the combined separate 2006 calculated liability. (i.e. His separate 2006 tax liability / (his + her separate 2006 tax liability) x actual married filing joint 2006 tax liability)
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