Mix almonds, chives, parsley, and 1 tablespoon oil in a small bowl; season with salt and pepper. Set aside.
Heat remaining 1/4 cup oil in a large pot over medium heat. Cook garlic and red pepper flakes, stirring occasionally, until garlic is softened, about 2 minutes. Add wine, bring to a boil, and cook until reduced by half, about 2 minutes.
Add clams and increase heat to medium-high; cover pot. Cook, shaking pot occasionally, until clams have opened, 5–8 minutes (discard any that do not open).
Meanwhile, cook pasta in a large pot of boiling salted water, stirring occasionally, until al dente. Drain, reserving 1 cup pasta cooking liquid.
Add pasta and 1/2 cup pasta cooking liquid to clams and toss to coat. Cook, tossing and adding more cooking liquid as needed, until sauce coats pasta, about 2 minutes; season with salt and pepper.
Serve linguine and clams topped with reserved almond-herb mixture.