Algae needs 3 things to grow:
1. carbon dioxide
2. phosphates and nitrates
3. light
Reduce any of these and it will help reduce algae.
I don't know what type of filter you have, but increasing the oxigenation of your water, decreasing the light period and/or reducing the level of nitrates / phosphates will help.
Also, I have found that cheap light bulbs (ex: Aqua glo) seem to produce the brown and red algae while bulbs like Coralife 50/50 produce more green algae.
I would also check you Nitrate levels.