[ensembl-dev] Finding the species that genes were lost from, in a Compara gene tree

[Avril Coghlan]

Dear Mathieu,

Thanks very much, that's very helpful. I've managed to pull out the list of lost taxa at a node now. 
Thank you!

Kind Regards,
Avril

On 22 Apr 2014, at 17:21, Matthieu Muffato <muffato at ebi.ac.uk> wrote:

> Dear Avril,
> 
> These ids relate to the species-tree that was used to guide the gene tree building. You can find them in the database in the species_tree_node table. With the API, you can use SpeciesTreeNodeAdaptor::fetch_node_by_node_id() to directly fetch the species-tree node, or if you already have a SpeciesTree object (by calling $gene_tree->species_tree for instance), you can do $species_tree->root->find_node_by_node_id($id)
> 
> Hope this helps,
> Mathieu
> 
> On 22/04/14 17:13, Avril Coghlan wrote:
>> Dear Ensembl developers and users,
>> 
>> I'm involved in some helminth genome sequencing projects in my group,
>> and my colleague (Eleanor Stanley) has built an-house Compara database
>> for these genomes.
>> 
>> I'm interested in identifying gene losses in the gene trees, and noticed
>> that some nodes have 'lost_species_tree_node_id' tags, with the node id.
>> of lost species in the species tree. These ids. are numbers, eg. 40001150.
>> 
>> However, I'm wondering how do I find out which species a particular
>> species tree node id. (eg. 40001150) corresponds to?
>> 
>> I will be very grateful for any help.
>> 
>> Regards,
>> Avril
>> 
>> Avril Coghlan
>> Parasite Genomics Team
>> Sanger Institute
>> 
>> 
>> 
>> 
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