Has anyone ever had to replace their clear out (sewer line from house) because of tree roots? What were the costs and any companies to recommend? 

Yes we had to do this last year. We used Lakeside plumbing. They did a great job and were honest and reasonable. It cost us $4000. 

Get more than one bid,did they run a camera down it, do search on here for plumber reviews,think Alfa omega gets good reviews. 

The city of Houston replaced mine. Suddenlink's had ran a cable line through ours and the city said the main sewer line and six feet out is their responsiblity to fix. 

Yes get bids.... we got several.