If you are dealing with a manual action link penalty, that doesn’t mean that you are not impacted by the Google Penguin algo.  A website can be impacted by both Penguin and a manual action for links at the same time.

The question was brought up on Twitter:

can a site be affected by Manual link penalty and Penguin at same time? i.e. even if mlp is removed its still penalised by Penguin?

Gary Illyes from Google responded and confirmed that it is possible to be hit with both Penguin and link related manual actions.

yes, it’s certainly possible a site is affected by penguin and also has a manual action for links related issues

While many experts were already aware this was a possibility, it is worth mentioning, especially for those who have fixed a manual action for links but are still presumed to be under the Penguin algo as well.

Penguin will be moving to a real time Penguin algo with the next update, so this does also mean that those with manual actions and Penguin can fix those issues much faster than before.