How to explain Strainphlan treeshrink parameter output

Hello, I’m using strainphlan with –treeshrink parameter. I found that this parameter create a treeshrink folder. I suppose the file with suffix TreeShrink.tre in the folder is the final output. But when I open it in R , I found it was a multiphylo object with two trees . I wonder which file is really the final output tree after treeshrink? THANKs!