[ensembl-dev] Gene Tree ambiguous nodes

[Sébastien Moretti]

Okay

Thanks Matthieu

> 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
SIB Vital-IT EMBnet, Quartier Sorge - Genopode
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