This allows you to enter one epoch-period combination, and up to ten phases. The subsequent extract command will use the union of all these phases to filter the data. If there is a phase file already present, you are given the chance to save it before proceeding.
XSELECT > filter phase epoch period phase <save_file>
The epoch is in MJD, the period in days, and the phase(s) run from 0-1.
So to filter using the epoch 40000, period of .5 days, and the first and third quarters of the period, say
XSELECT > filter 40000 .5 "0.0-.25,0.5-0.75"
The " "'s are necessary to protect the comma.