Heat the oil in a very large pot over medium heat. Add the onion, garlic, oregano, and red pepper flakes. Saute' until the onion is tender, about 10 minutes.
Add the tomatoes with their juice, clam juice, and wine. Bring to a boil over high heat. Decrease the heat to medium and simmer uncovered until the liquid reduces by one third, about 30 minutes.
Add the clams, cover, and simmer over medium-high heat, stirring occasionally, just until the clams open (discard any clams that don't open), about 8 minutes. Remove the pot from heat. Using a slotted spoon transfer the clams to a large bowl and cover to keep them warm. Stir the parsley and butter into the pot.
Meanwhile, bring a large pot of salted water to a boil. Add the linguine and cook, stirring frequently to prevent the pasta from sticking together, until tender but still firm to bite, about 8 minutes.
Drain. Ad the linguine to the sauce and toss until the sauce thickens slightly and coats the linguine. Season the pasta generously with salt and black pepper. Transfer to bowls and tops with clam sauce and serve.