SPTK has several commands for spectral analysis, but not all the commands allow to use spectrum as the input of the command. The following commands are the candidates that support spectrum input:
fftcep
uels
lpc
acorr
Since lpc and acorr calculate autocorrelation sequences in time domain, the calculation should be done in frequency domain using FFT to avoid numerical error caused by the mismatch between the two domains. Note that adaptive analysis-based commands, acep, amcep, and agcep, cannot handle spectrum as the input due to the framework.
SPTK4 solved the problem.