[ensembl-dev] Gene Tree ambiguous nodes

Matthieu Muffato muffato at ebi.ac.uk
Tue May 17 00:27:31 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

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

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
> http://bioinfo.unil.ch/
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