A good way to kill tree roots in your sewer line is to take some rock salt and flush it down the toilet.
You should flush at least 2 pounds of rock salt down the toilet for it to be effective.
The rock salt will dry out and kill the roots.
Alternatively you could put the rock salt in your sewer clean out and flush it down the sewer line with a water hose.
It's also a good idea to run a hose down your sewer clean out to let fresh water push any residue out of your sewer every so often.
I run a hose to flush my sewer line out at least every 6 months to help keep it clean and add some rock salt in the process to help keep tree roots away.