[Bioperl-l] Bio::Tree::Tree -- rerooting & bootstrap problem

[Bank Beszteri]

Dear Bioperl folks,

I´m trying to use Bio::Tree::Tree for manipulating phylogenetic trees, 
but in some things it did not behave as I expected it to, so I had to 
look inside a bit.
In particular, I had problems with mixed up bootstrap values after 
re-rooting. After looking into the Bio::Tree::Tree data structures, it 
seems that

a) bootstrap values are stored as attributes of nodes of the tree [to my 
understanding, they should rather be attributes of branches but 
Bio::Tree::Tree apparently tries to simplify away branches]; each node 
stores the bootstrap value belonging to the branch that connects it to 
its ancestor node (I´m reading in trees from Newick strings, and 
bootstrap values arrive in the id fields of internal branches)

b) when re-rooting a tree, bootstrap values stay with the same node 
where they were before. Because the node that used to be the ancestor of 
a particular node in the original tree might have become its descendant 
after re-rooting, the bootstrap values are being mixed up.

Can you confirm my conclusion? Whether yes or no, have you got an easy 
workaround or alternative solution to re-rooting trees (without having 
to touch the reroot method) or any other hints that could be useful for 
me to deal with this issue?

Cheers,

Bank



--
Dr. Bánk Beszteri
Alfred Wegener Institute for Polar and Marine Research