The end-to-end encryption that will be found in Google's upcoming messaging app Allo will be powered by Open Whisper Systems Signal Protocol. Conversations that are held in Incognito mode will be fully encrypted, and disappear once you exit Incognito.
Very little was said during the original announcement about how the end-to-end encryption would work, or who Google partnered with to provide the security. From Open Whisper Systems announcement:
We're excited to partner with Google on the private communication features of their new smart messaging app, Allo. We've been collaborating together on the integration of Signal Protocol into Allo, which will bring all of Signal Protocol's strong encryption properties to Allo's incognito mode.
Open Whisper Systems said it will provide further details on the integration once the app is officially available from Google later this summer.