This paper presents, by example, an index theory appropriate to algebras without trace. Whilst we work exclusively with the Cuntz algebras the exposition is designed to indicate how to develop a general theory. Our main result is an index theorem (formulated in terms of spectral flow) using a twisted cyclic cocycle where the twisting comes from the modular automorphism group for the canonical gauge action on the Cuntz algebra. We introduce a modified $K_1$-group of the Cuntz algebra so as to pair with this twisted cocycle. As a corollary we obtain a noncommutative geometry interpretation for Arakis notion of relative entropy in this example. We also note the connection of this example to the theory of noncommutative manifolds.
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