To each tagged triangulation of a surface with marked points and non-empty boundary we associate a quiver with potential in such a way that whenever we apply a flip to a tagged triangulation the Jacobian algebra of the quiver with potential (QP) associated to the resulting tagged triangulation is isomorphic to the Jacobian algebra of the QP obtained by mutating the QP of the original one. Furthermore, we show that any two tagged triangulations are related by a sequence of flips compatible with QP-mutation. We also prove that, for each of the QPs constructed, the ideal of the non-completed path algebra generated by the cyclic derivatives is admissible and the corresponding quotient is isomorphic to the Jacobian algebra. These results, which generalize some of the second author’s previous work for ideal triangulations, are then applied to prove properties of cluster monomials, like linear independence, in the cluster algebra associated to the given surface by Fomin, Shapiro and Thurston (with an arbitrary system of coefficients).

We study the dependence of a cluster algebra on the choice of coefficients. We write general formulas expressing the cluster variables in any cluster algebra in terms of the initial data; these formulas involve a family of polynomials associated with a particular choice of ‘principal’ coefficients. We show that the exchange graph of a cluster algebra with principal coefficients covers the exchange graph of any cluster algebra with the same exchange matrix. We investigate two families of parameterizations of cluster monomials by lattice points, determined, respectively, by the denominators of their Laurent expansions and by certain multi-gradings in cluster algebras with principal coefficients. The properties of these parameterizations, some proven and some conjectural, suggest links to duality conjectures of Fock and Goncharov. The coefficient dynamics leads to a natural generalization of Zamolodchikov's $Y$-systems. We establish a Laurent phenomenon for such $Y$-systems, previously known in finite type only, and sharpen the periodicity result from an earlier paper. For cluster algebras of finite type, we identify a canonical ‘universal’ choice of coefficients such that an arbitrary cluster algebra can be obtained from the universal one (of the same type) by an appropriate specialization of coefficients.