Cook linguine in salted water until al dente or desired doneness. Drain; reserve.
Saute the shallots in olive oil over medium heat in a large, shallow pan with a tight fitting lid. Cook until they are softened, about 5 minutes. Add in the garlic and cook for about 1 minute until fragrant.
Add in the Manila clams and stir just until they begin open up. Add in the chopped clams, cream and season with salt and pepper. Cover the pan and cook until the Manila clams have opened up. Add in the butter, and stir until it has all melted and the sauce is mixed.
Place a the pasta in each serving dish. Top each plate with some clams and some of the sauce. Sprinkle grated cheese, parsley, and basil over the top before serving. If you are looking for a little kick sprinkle pepper flakes, too.