There are lots of sampling ADCs which will support that type of
operation directly or you can easily design and build a sampling phase
detector but that all involves significant extra circuitry outside of
the microcontroller.

Take a look at the Racal Dana 1992 reference frequency multiplier
option (the schematic is on page 7-33 of the service manual) for an
example of a sampling phase detector used in a similar application.

On Thu, 6 Dec 2012 16:43:26 -0800, Chris Albertson
<albertson.ch...@gmail.com> wrote:

>What if the OCXO had a sine wave output and then you used the PPS leading
>edge to gate the sine wave to a sample and hold.  then the sample is
>measured by the Arduino's ADC?  I think(?) you get a 10-bit ADC or is it
>8-bits.  The problem is the required speed of the sample and hold, maybe
>not easy to build

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