I was trying to write a script to design primers for PCR multiplexing when I ran upon these programs that were already made for the same reason. However, my question is which seems to be the better pick? From my review, they both use primer3 to design the primers, although MPprimer uses MFEprimer to further analyze primer interactions while PCRTiler uses BlastN.
You can write a pipeline for design multiplex PCR primers with primer pick software (e.g. Primer3), primer specific checking program (e.g. MFEprimer) and primer secondary structure checking program (e.g. use ntthal to check self-dimer, cross-dimer, hairpin).