You need to be a bit more specific. Are you interested in seeing if a given tree is a subtree of another? I'm assuming that this is what you want.
The R library
ape will return all subtrees for a given tree (http://svitsrv25.epfl.ch/R-doc/library/ape/html/subtrees.html). I imagine an algorithm structured in the following way:
1. Read in a tree and estimate all subtrees of that tree. Store the subtrees as an object.
2. Calculate a distance metric from your tree to each one of the subtrees. The
phangorn library (and others) will calculate the standard bipartition distance (Robinson-Foulds) between pairs of trees; if there is a distance of zero from your tree to one of the subtrees, you know that your tree is identical in branching structure to that subtree.
This can be easily accomplished in R. Hope this helps.