I don't know of any MATLAB code, but I believe the LyapOde software linked at the bottom of Paul Bryant's page may implement what you want. It is written in C. From its documentation:
The software also supports the calculation of Conditional Lyapunov Exponents or CLEs (see Pecora et al, Chaos Vol. 7, No. 4, (1997), 520). The CLEs are the Lyapunov exponents of a response system that receives unidirectional synchronizing stimulus from an identical drive system. Three types of stimulus are considered: continuous coupling, periodic impulse coupling, and substitution (full or fractional). More details are given in the discussion section below. The synchronizing stimulus can be applied to one or more of the variables. When any of the CLEs are positive or zero, they can be calculated in both synchronized and unsynchronized mode which typically give differing results. In the latter case the drive and response systems are allowed to freely deviate away from synchronization.
Currently the software includes the equations for the standard Lorenz model, the Rossler system, the Rossler hyperchaos system, the 5-variable version of the Lorenz cyclic 1996 model, the Colpitts oscillator, and the driven Van der Pol oscillator.