Is it possible to encrypt the boot disk in El Capitan?
It's possible to encrypt the entire system volume with FileVault 2 -- open System Preferences -> Security &amp; Privacy pane -> FileVault tab, and click Turn On FileVault. I'll walk you through some setup questions (most important: set up an emergency recovery option, either by linking to your iCloud account or by generating a random key you should write down and store someplace safe), then restart the system and begin encrypting the volume in the background.

This isn't quite full disk encryption, because it leaves the (hidden) Recovery HD partition unencrypted. Recovery HD contains emergency repair/reinstall tools, as well as the booter that's used to unlock and start up from the main (encrypted) volume. But no user data gets stored in Recovery HD, so this isn't a significant weakness.