[ensembl-dev] Gene Tree ambiguous nodes

Matthieu Muffato muffato at ebi.ac.uk
Tue May 17 10:57:19 BST 2011

Hello Sébastien

In the database, the value is stored in the protein_tree_tag table (tag:
"duplication_confidence_score"). It can be retrieved with the following
API method: $node->get_tagvalue("duplication_confidence_score");

Matthieu Muffato

>> 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.
> Okay.
>> 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
> http://bioinfo.unil.ch/

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