[BioRuby] BioRuby Phyloxml update

[Tomoaki NISHIYAMA]

Hi,

One point seems that tree can be unrooted or rooted.
Perhaps, Goto-san's Bio::Tree represents unrooted tree (not  
distinguishing parents and childrenn),
while Diana's class is for rooted trees (having distinction of  
parents and children).
If, this is the point, Bio::RootedTree is better name than  
Bio::FamilyTree.
In general, rooted tree should be easily converted to unrooted tree,  
while
conversion of an unrooted tree to rooted tree requires specification  
of the root.

For text representation like NEWICK there is anyway a root while
the tree can be interpreted either as rooted or unrooted.

It could be good to have distinct interface for rooted and unrooted  
trees,
to let the user's be aware of the conceptual difference.
-- 
Tomoaki NISHIYAMA

Advanced Science Research Center,
Kanazawa University,
13-1 Takara-machi,
Kanazawa, 920-0934, Japan