When I updated my workstation to El Capitan, I could not see the serial ports for my Alien FCs and USBasp programmers anymore.
Here is the solution: https://www.kiwi-electronics.eu/blog?journal_blog_post_id=7
Just in case above post disappears at some stage, here is the important bit:
Reboot and press CMD+R immediately after hearing the startup sound to boot to Recovery Mode
Execute the following command: csrutil enable --without kext