You have to program the timers directly to select antiphase outputs from the pins connected to a timer.
On the Uno and other ATmega328 based arduinos the pins 9,10 are driven from timer1 and can be
set to work in antiphase. Similarly 5,6 for timer0 and 11,3 for timer2.
Look at the documentation in the chip's datasheet for TCCR1A, TCCR1B etc.