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After the voice is converted into the form desired for transmission it must be assembled in an orderly way, following a specific protocol. In most networks there are layers of protocol each on top of the other and this is referred to as the protocol stack. (You can think of this as a bit like a Russian nested doll.) Some aspects of the signal transmission only need an outer protocol, but eventually at the end point all layers need to be stripped and then decoded by the vocoder, etc.
For one network or one end point to talk to another the protocols must align or you cannot communicate. Sometimes you may wonder why some method does not work with another and you can be pretty sure that there are likely incompatible protocols or vocoders preventing communication. Since we are still in an early phase of VoIP this will be the case for some time, and may always be an issue.
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