I am assuming you have built a tree using the -maketree and neighbor-joining options of MUSCLE. There are two commonly used easy ways of rooting a tree: one is to define an outgroup, the other is called midpoint rooting and places the root in the middle of the segment between the two most distant leaves. For more details on rooting trees, see this book chapter. As for doing it in practice, you can use the root() function from the R package ape.