We describe for the first time in the scientific literature the Planetary Ephemeris Program (PEP), an open-source general-purpose astrometric data analysis program. We discuss, in particular, the implementation of pulsar timing analysis, which was recently upgraded in PEP to handle more options. This implementation was done independently of other pulsar programs, with minor exceptions that we discuss. We illustrate the implementation of this capability by comparing the post-fit residuals from the analyses of time-of-arrival observations by both PEP and Tempo2. The comparison shows substantial agreement: 22 ns rms differences for 1,065 pulse time-of-arrival measurements for the millisecond pulsar in a binary system, PSR J1909-3744 (pulse period 2.947108 ms; full-width half-maximum of pulse 43 $mu$s) for epochs in the interval from December 2002 to February 2011.
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