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

[Matthieu Muffato]

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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