I asked my scope expert.  His advice was:

1) measure the period of the signal T1
2) Measure the time between the rising edges of the two signals T2
3) calculate the phase in degrees as  (T2/T1) * 360

He was not certain whether or not these were automatic measurements on
the 54201.

But many Agilent scopes do have a way to acquire signals on channel
1&2, find the period of channel 1, and find the rising edges of
channel 1 and channel 2 and obtain the difference.  (You just have to
calculate the phase yourself from the time information.)

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