The best replacement for fft is dft.

The best alternatives to fft are rated as following:
★★★★★  dft
★★★★  rta
★★★★  psd
★★★  ffta
★★★  dct
★★★  tactics ogre
★★  war of the lions
★★  fht
★★  mst
★★  power spectrum
★★  fourier transform
★  pwelch
★  wavelet
★  disgaea
★  alloderm
★  convolution
★  spectrum analyzer
  ffta2
  pmma
  fftw
  belladerm
  blend prime95
  floating point fft
  real fft

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Google Trends

Scale is based on the average worldwide traffic of fft in all years. Click on graph for more.
fft
dft
rta