You can determine the phase shift and duty cycle for the required clocks when using ALTLVDS_RX and ALTLVDS_TX in external PLL mode by first compiling an example design with ALTLVDS_RX or ALTLVDS_TX using an internal PLL. Use the settings that the Quartus® II software uses to configure the internal PLL in the example design as the settings you enter in the external PLL.
To check the PLL settings in the Fitter report, expand the Resource section, and then expand PLL Usage. The report shows the duty cycle, phase shift and clock frequency for each of the required clocks for the ALTLVDS_RX and ALTLVDS_TX interfaces. You can then use these parameters for the external PLL settings in your design.