That depends on the position of your wisdom teeth.
If the position of your wisdom teeth does not affect treatment, we can usually leave them in.
If your treatment requires molar distalization (molar teeth to be moved), then the wisdom teeth will need to be removed.
Do consult your orthodontist so that he/she can have a thorough examination of your dental condition (clinically and radiographically) and advise accordingly.
For the removal of your wisdom teeth, your orthodontist will generally refer you to an oral surgeon (dental specialist in oral & maxillofacial surgery) or a general dentist if the case is not complex or severely impacted.