[Bioperl-l] Bio::TreeIO: Problem rerooting with a leaf

Ferdi ferdinand.marletaz at gmail.com
Thu Feb 11 11:41:01 EST 2010


Hi-
I am an enthusiastic user of Bio::TreeIO module, and I got some
problems with it after a recent reinstall of bioperl on my new mac
(10.6, previous was 10.5).  Particularly, when attempting to reroot
($tree->reroot($leaf))  a tree with a leaf node, it doesn't seem to
consider ianymore t as an outgroup but as the root itself... For
example, with the example provided on Howto bioperl page:
(((A,B),(C,D)),E);
what I get when reroot with A:
((B,((C,D),(E))))A;
while I should get something like:
(A,((E,(C,D)),B));
with A considered as outgroup instead of the root node itself.
Thanks for your help!
Ferdi


More information about the Bioperl-l mailing list