[Biopython] tree traversal

[Jessica Grant]

Hello,

I have been working with phylogenetic trees, and am trying to write a
script that traverses the tree and returns sister taxa to monophyletic
clades.  I've been using the Phylo module in Biopython, but find it
confusing.

Briefly, my script takes all leaves and checks to see if the parent clade
is monophyletic based on the names of the leaves.  If so, it checks the
parent of that clade, and so on.  When it gets to a clade that is
non-monophyletic, it should return the name of the leaf or leaves that
aren't in the monophyletic group.

Phylo seems to give spurious results (or at least results that I don't
understand) having to do, maybe, with the way it traverses the tree.
 Sometimes it seems to work fine, but other times it returns taxa that,
looking at the tree, don't seem to be the nearest neighbors.

I was wondering if anyone has worked with this module and might have some
advice...or if there is a better way to approach this problem.

Thanks,

Jessica