Can my supervisor use my code in his paper without acknowledging me?
A lot of questions here are left unanswered.

Are you a student?  A staff programmer?  Do you have a work-for-hire agreement with the university?  Is it just your implementation, or is it your original synthesis of several algorithms?  Is the synthesis something that is novel &amp; not obvious and do you think it constitutes a significant intellectual contribution?  Have you previously published about this synthesis and if so is that cited?  How core is the use of these algorithms to the main results of the paper?  

It might be reasonable to point out to your advisor how it would be helpful to your career (ability to get a great job after leaving, etc.) if your contributions are recognized in the papers that use them, at least in the acknowledgements section.  It may be that for whatever reason the supervisor hasn't thought of this (or doesn't remember when writing it up close to the deadline) but may be very willing to do so. 

If you are a student and the supervisor is your academic advisor, you may also ask questions/have a conversation about what authorship means in your field and what the expectations are for what contributions warrant authorship in your collaborations.  Part of an academic advisor's role is to teach their students about these sorts of things. 

If you don't feel comfortable with a direct conversation or with the results of one, go to your program director and see what their perspective might be.