[ensembl-dev] Gene Tree ambiguous nodes

Sébastien Moretti sebastien.moretti at unil.ch
Tue May 17 10:34:42 BST 2011

> Hello Sébastien
> An ambiguous node is a duplication node with a duplication confidence
> score of 0. It means that the two resulting copies of the duplication can
> not be found at the same time in the same species. There is indeed a
> correlation with the bootstrap value, but the latter isn't use in the
> definition.

Do you know where this duplication confidence score is stored in the 
compara database ?
Or how to access it through the ensembl API ?

> Right now, at most one lost taxon id is stored in the database. So the the
> API cannot help you to retrieve the full information, you'll have to
> rebuild the list of lost taxa by comparing the gene trees to the species
> tree.


> Regards
> Matthieu Muffato
>> At the same time, do you store lost taxa in trees (NHX) as TreeFam does ?
>>> Hi
>>> I wonder how ambiguous nodes are defined in gene trees.
>>> Nothing seems to be attached to the D flag in NHX labels for ambiguous
>>> nodes.
>>> ambiguous nodes seem to be related to bootstrap values.
>>> Is it true ?
>>> If true, what is the bootstrap threshold you use to define a node as
>>> ambiguous ?
>>> Regards

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

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