Allen overcame the heat and the wind to turn in a 7-under 63 at the Omaha Country Club, putting him at 10-under 130 for 36 holes.
Only nine players reached the midway point of the tournament with a sub-par total.
Allen has one major title to his credit on the Champions Tour, that victory coming at the Senior PGA Championship four years ago. He played the front nine in 30 strokes, did not make a bogey all day and his round was highlighted by an eagle at the par-5 14th.
Allen was one of seven players who shared the lead after the first round.
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