Algae only becomes an issue when it develops so heavily on the top surface of the medium that it clogs up airflow to the root system, which likely won't happen between repotting jobs.. Other than that, it is just an aesthetic issue.
If you simply don't want it there, you may drop the clear pot into an opaque one for growing (you can still lift it out to check the roots), or you can do a periodic drench with an algaecide (every 4-6 weeks is fine). Ones known to be effective are chlorine bleach (one ounce per gallon), Physan (1 teaspoon per gallon), or something like Zero-Tol or Oxi-Date, which are hydrogen peroxide that has been stabilized for horticutural applications. I don't think drugstore H2O2 will be al that effective, as it decomposes so rapidly.
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