Dear Nick,

"Tree comparison" in HyPhy assumes that both trees have the same set of tip labels, so it doesn't directly apply to comparing trees from two different organisms.

There are several things you could try (for general trees)

1). Compute some tree statistics (the asymmetry indices) using Tree->Additional Tools->Tree Statistics

2). Investigate branching patterns using Stochastic Context Free Grammars (like it was done in http://mbe.oxfordjournals.org/cgi/content/abstract/22/4/905). Art and I have implemented some (yet) undocumented SCFG code in HyPhy, so it can be used to compare the grammars induced by each of the trees. If you are interested, I can post some sample HyPhy batch language code and an updated HyPhy build which enables you to do that.

If you have a specific objective for tree comparison in mind, let me know, and I may be able to give you further advice.

Cheers,
Sergei