I want to generate an FSK signal with a radio. My first idea is to generate an audio in which the high level is a 1 and the low level is a 0:

Audio generated by MATLAB

This audio is then modulated by the radio with FM. In theory I think it should work, as FSK is just modulating the binary packet, but I see that programs like MixW generate an audio completely different from what I generated:

enter image description here

What is the proper way to generate an audio which will input a radio to obtain an FSK modulation?

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    $\begingroup$ I personally don't use MixW, so this is not 100% sure, but did you check how did they actually intend the program to be used? Usually, you connect such program to a radio in single-sideband mode, which acts as a frequency up-converter. The result is that you need to actually feed it a frequency modulated signal baseband, in order for the RF signal to be frequency modulated as well. The discontinuities in the second image look a little bit like the artifacts that appear due to change of frequency. $\endgroup$ – AndrejaKo Jul 6 '15 at 10:10

The whole idea is to use 2 (or more for MFSK) tones to modulate the signal. As long as the tones are the correct frequencies it works. You can use standard tones and no need for special equipment to detect the tones or use non-standard tones and make your own detectors. Either way works. I had a schematic when I was younger (about 40 years ago) that used opamps configured as cascaded Butterworth filters to do the job. it then went to a Timex/Sinclair 1000 computer with A whopping 2K of memory and the program encoded and decoded it for you. You could tune them to ANY frequency you wanted, but the parts used were for the standard frequencies.

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