I tested spek, freqtweak, sndfile-spectrogram (sndfile-tools), jaaa, xoscope, but baudline seemed to be the best one.
Baudline isn't in the Ubuntu repos so you have to download it from the link above.
Since I wanted to analyze a sine wave generated by AMS, I ran baudline_jack (instead of baudline).
Here's a screenshot showing the frequency of a sine wave generated using AMS, using a VCO set to octave 3.
If you mouseover the white left to the left, you'll see the frequency at the right--in this case, a sine wave set to octave 3 in ams generates a tone at ~150 Hz, which is near a D3 note.
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