[ensembl-dev] Gene Tree ambiguous nodes

[Matthieu Muffato]

Hi Sébastien

The value must be 0 to define a node as ambiguous

Matthieu Muffato

> Thanks Matthieu
>
> What is the threshold to define a node as ambiguous ?
> Value range seems to be between 0 and 1
>
>> 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");
>>
>> Regards,
>> 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/
>