In a deep skillet cook the shallot and the garlic in the butter over moderate heat, stirring, until they are pale golden, add the flour, and cook the mixture, stirring, for 1 minute. Stir in the wine, the bottled clam juice, and the clams with the juice and simmer the sauce, stirring, for 5 minutes. Stir in the parsley, the thyme, and salt and pepper to taste and keep the sauce warm. In a kettle of salted boiling water boil the linguine until it is al dente, drain it, and in the skillet toss it with the clam sauce.
