In a large pot bring salted water to a boil. Cook the pasta 1 minute less than the al dente directions. Reserve about ½ cup of the starchy pasta water, drain using a colander, but do not rinse the pasta.
While the water is boiling add the olive oil to a pan over medium high heat. Add the shallots and cook until soft, about 2-3 minutes. Add the garlic and cook for another minute.
Add the wine, capers, parsley, pepper flakes, pepper, and clams, reduce the heat to medium and cover. Cook for 3-5 minutes or until the clam open up, and discard any unopened clams.
Add the pasta to clams and gently toss. Add ¼ cup of the pasta water and toss until all of the pasta is coated. Add the butter. Once melted remove from the heat and add the lemon juice and lemon zest and toss for a final time.