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In this paper, we describe and analyze the design of a joint Transport, routing and spectrum sharing (TRSS) optimization algorithm for wireless networks with frequency- agile radios. We capitalize on the spectrum agility of modern radios which can configure both the central frequency and spectrum width of their channels. TRSS is fully distributed and is executed in two phases. In the first phase a dual driven optimizer is used to jointly adjust end-to-end transmission rate, flow-routing and spectrum width allocation. In the second phase, an innovative timing-window based spectrum access scheme is used for link layer scheduling. Analytical and simulation results show the effectiveness of our design.