[Bioperl-l] TreeIO altering tree topology

[Aaron J Mackey]

The good news: I've written an TreeIO/nhx.pm to handle Chris Zmasek's New
Hampshire eXtended (NXH) treefile format.  This allows trees to be stored
including "tagged" values like Bootstrap, Species, EC number, etc.  See:

http://www.genetics.wustl.edu/eddy/forester/NHX.html

The bad news: in testing out my parser, I've found that newick.pm (and, by
extension, nhx.pm) alters the topology (branching order) of this input
tree:

(((hADH2:0.1,hADH1:0.11):0.05,nADHY:0.1,iADHX:0.12):0.1,(yADH4:0.09,yADH3:0.13,yADH2:0.12,yADH1:0.11):0.1);

into this:

(yADH4:0.09,yADH3:0.13,(hADH2:0.1,hADH1:0.11):0.05,(nADHY:0.1,iADHX:0.12):0.1,(yADH1:0.11,yADH2:0.12):0.1);

I've tried to convince myself that these two are the same topology, and
that everything is fine, but I cannot.

Upon further inspect of the built tree, it looks like the tree itself is
misformed (i.e. it's not an output problem).  I haven't been able to find
what's going wrong, so I thought I'd shoot it out to the rest of you.

-Aaron