The DOS versions of trunker hooks the interrupt service routine for IRQ 3 or 4, depending upon which COM port the program is trying to monitor. The UART can be configured to generate an interrupt each time one of the modem status input pins like DCD, DSR, CTS, or RI changes. Trunker measures the time between interrupts to determine the presense of a 1 or 0 pulse (or consecutive pulses). It does not examine data from the RXD pin at all.
As far as I know, the serial UART drivers for Linux do not support this type of functionality. I think this is why we haven't seen a Linux version of trunker so far (or a native OS-X MAC version, either).
This leaves you with either (a) using sound input or (b) writing your own kernel mode driver module. You might be able to take the standard Linux UART drivers and modify them to accept some custom IOCTL commands to pull the interrupt timing from the UART.
Regards,
Rick