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there are several different reasons this could happen. If they are stressed for any reason they may get pale. Also, substrate color can have an effect on how vibrant their colors look as well.
Well to update, I have put all of my males in one tank and all of the females in the other tank. Now my female once again has her bubble sticking out of her rear it was getting better until I moved her any ideas?
I checked my water and its great. I'm still not sure what to do about my female. When this first happened I added more salt to my tank which helped her but almost killed my algea eater. How do I treat her without hurting my other fish?