Fldigi operates (as does most similar software) in conjunction with a conventional HF SSB radio transceiver, and uses the PC sound card as the main means of input from the radio, and output to the radio. These are audio-frequency signals. The software also controls the radio by means of another connection, typically a serial port.
Fldigi is multi-mode, which means that it is able to operate many popular digital modes without switching programs, so you only have one program to learn. Fldigi includes all the popular modes, such as DominoEX, MFSK16, PSK31, and RTTY.