In a large pot, bring to a boil 6 quarts of salted water. Add pasta, stirring constantly in the beginning to prevent it from sticking together. Cook until al dente, about 8 minutes.
Meanwhile, heat the olive oil in a large saute pan. When almost smoking, add shallots and garlic and saute until soft and translucent, about 3 to 4 minutes, being careful not to burn the garlic. Add the clams, red pepper flakes and wine. Cover and simmer for 6 to 8 minutes or until most clams have opened.
Add 2 tablespoons chopped parsley. Whisk in butter to thicken sauce slightly.
Drain pasta in a colander. Do not rinse pasta with water - this will remove the pasta's natural starches. Place pasta into the clam saute pan and mix thoroughly. Check seasoning.
Pour pasta into large serving bowl. Zest lemon over the dish, being carefull not to zest the white part of the lemon, which is bitter.
Garnish with remaining parsley. Serve immediately.
Sprinkle with parmesan reggiano, if desired.