If you want to time with specific inputs, on your system, as currently configured, with the current load, then you can use http://www.mathworks.com/matlabcentral/fileexchange/18798-timeit-benchmarking-function
If you are trying to do an analysis of how the time varies with the size of the inputs, then in the general case you cannot do that. "Order analysis" needs to be done algebraically and through use of theorems.
