Using makefile facility with code composer studio

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Can we use any version of MATLAB with 'Embedded Encoder' facility to work with any version of code composer studio?I have MATLAB 2007b and CCS 3.1 which are not compatible with each other,if I am right.I want to run one MATLAB program(not Simulink model) & one Simulink model on DSK 6713.Please help me!

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