[ensembl-dev] protein tree id and tagvalue

Moretti Sébastien sebastien.moretti at unil.ch
Wed Jul 4 15:10:38 BST 2012

> children() returns the children of a node in a random order as given by
> the database, that may vary from one call to another.
> sorted_children() returns the same children, but in a stable and
> reproducible order.
> In your case, you can call any of these two methods, but on $tree (which
> is at this stage a GeneTreeNode).

But $tree is not a GeneTreeNode object, it is a GeneTree object in my case:
my $tree_adaptor = $reg->get_adaptor('Multi', 'compara', 'GeneTree');
my $tree         = $tree_adaptor->fetch_by_root_id(487410);

Bio::EnsEMBL::Compara::GeneTree=HASH(0x2a85b40) does not understand 
method Bio::EnsEMBL::Compara::GeneTree::children

In the documentation I only see root method that returns a GeneTreeNode 
object from a GeneTree object.

> The code to select subtrees of the appropriate clade should actually be
> the same as in previous releases. I think only the initial call to get
> the list of root nodes is different (+ the interpretation of the
> "Duplication" tag)
> Matthieu

Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/

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