Fill a large pot with lightly salted water and bring to a rolling boil over high heat. Once the water is boiling, stir in the linguine, and return to a boil. Cook the pasta, stirring occasionally, until cooked through but still slightly firm, about 11 minutes. Drain well.
Heat the butter and olive oil in a skillet over medium heat until it begins to brown slightly. Stir in the onion; cook and stir until the onion becomes lightly golden, about 10 minutes. Stir in the garlic and cook for 1 minute more. Add the reserved clam juice and wine. Simmer until reduced by half, about 15 minutes. Stir in the Alfredo sauce and clams; cook and stir until heated through, about 5 minutes.
Serve the clam sauce over the linguine, and sprinkle with Parmesan cheese and red pepper flakes.