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In this paper, we propose and study a novel cooperative communication system combined with software-defined radio (SDR) in heterogeneous networks. SDR enables a terminal to exploit multiple heterogeneous links with minimized hardware cost. Compared with that in conventional cooperative communication systems, each node in the proposed system dynamically reconfigures a transmission protocol in each cooperation phase to maximize the attainable data rate. We present an analytical framework for the selection and reconfiguration of a transmission protocol and evaluate the gains of the proposed system in terms of spectral efficiency and outage probability. Owing to extra degrees of freedom by multiple reconfigurable access terminals (RATs) in SDR, the cooperative diversity gain is significantly enhanced.