[ensembl-dev] Gene Tree ambiguous nodes

[Sébastien Moretti]

> 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/