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We study the cluster algebras arising from cluster tubes with rank bigger than 1. Cluster tubes are 2−Calabi-Yau triangulated categories which contain no cluster tilting objects, but maximal rigid objects. Fix a certain maximal rigid object T in the cluster tube C_n of rank n. For any indecomposable rigid object M in C_n, we define an analogous X_M of Caldero-Chapton's formula (or Palu's cluster character formula) by using the geometric information of M. We show that X_M,X_{M′} satisfy the mutation formula when M,M′ form an exchange pair, and that X_? : M↦X_M gives a bijection from the set of indecomposable rigid objects in C_n to the set of cluster variables of cluster algebra of type C_{n−1}, which induces a bijection between the set of basic maximal rigid objects in C_n and the set of clusters. This strengths a surprising result proved recently by Buan-Marsh-Vatne that the combinatorics of maximal rigid objects in the cluster tube Cn encode the combinatorics of the cluster algebra of type B_{n−1} since the combinatorics of cluster algebras of type B_{n−1} or of type C_{n−1} are the same by a result of Fomin and Zelevinsky. As a consequence, we give a categorification of cluster algebras of type C.

We introduce a homotopy theory of digraphs (directed graphs) and prove its basic properties, including the relations to the homology theory of digraphs constructed by the authors in previous papers. In particular, we prove the homotopy invariance of homologies of digraphs and the relation between the fundamental group of the digraph and its first homology group. The category of (undirected) graphs can be identified by a natural way with a full subcategory of digraphs. Thus we obtain also consistent homology and homotopy theories for graphs.