Try using a logic gate block or XOR the two signals. Alternately, pass the two sine waves firstly from a comparator/Schmidt Trigger to convert into a square wave and then XOR the two inputs to get an output proportional to the phase difference of the two input signals.

Best Luck!

Hi

I advice you to see this document. You will find what you need.

Best regards

http://fr.mathworks.com/help/signal/examples/measuring-signal-similarities.html

see this link - 

http://in.mathworks.com/help/comm/ref/complexphasedifference.html

just for clarification Matlab does not do Analog processing, but you can use very high sampling frequency.

At first, you need to convert to Digital signal then correlate them.

Example: Two signals-

x=[0 0 0 0 1 2 3 0 0];

y=[1 2 3 0 0 0 0 0 0]; %Here x has a lag of 4

xcorr(x,y) %peak at index=13=9+4

If their lenght is not equal,

x=[0 0 0 0 0 1 2 3 0 ];

y=[1 2 3 0 0 0 0 0 0 0]; %Here x has a lag of 5

xcorr(x,y) %peak at index=15=10+5=length of second signal+Lag

You need to multiply that index with sampling period for time difference.

Finally, phase difference=time difference*2*pi/Period.

It is computationally expensive for large signals and you can do downsampling for faster operation.