We show that for groups acting acylindrically on simplicial trees the K-and L-theoretic Farrell-Jones Conjecture relative to the family of subgroups consisting of virtually cyclic subgroups and all subconjugates of vertex stabilisers holds. As an application, for amalgamated free products acting acylindrically on their Bass-Serre trees we obtain an identification of the associated Waldhausen Nil-groups with a direct sum of Nil-groups associated to certain virtually cyclic groups. This identification generalizes a result by Lafont and Ortiz. For a regular ring and a strictly acylindrical action these Nil-groups vanish. In particular, all our results apply to amalgamated free products over malnormal subgroups.

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