[ensembl-dev] documentation missing

Andy Yates ayates at ebi.ac.uk
Wed Feb 13 10:21:01 GMT 2013

Hi Joe,

Since you're not a native Perl programmer have you tried looking at our REST API? We have two endpoints which may be of interest to you:


The first provides access to the GeneTrees in both Newick & PhyloXML; the later of the two also returning the protein/cds sequence of each member in the tree optionally aligned. The second endpoint gives you orthologs which is where, as Miguel pointed out, dnds is held. So to use your example (using PROCR):


Would give you the PhyloXML tree & nh trees. However we've used some prior knowledge that PROCR is in this GeneTree (this is a feature we will extend to asking for GeneTrees by their Gene).

Then to get the homologies for this gene (which can be restricted with other parameters):


Of course the REST API is a beta product so it may not provide enough information at the moment but please let us know how we can improve it.

Best regards,


Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 12 Feb 2013, at 16:02, Joe Carl <joseph.w.carl.jr at gmail.com> wrote:

> I'm reading the compara database scheme webpage (http://www.ensembl.org/info/docs/api/compara/compara_schema.html), and noticed the three most intersting functions (to me) are missing.
> where is the documentation for the following
> 	• species_tree_node
> 	• species_tree_node_tag
> 	• species_tree_root
> My goal is the following:
> 1) Grab the phylgentic trees already generated by ensemble (for specific Gene ID)
>      a) Newicks
>      b) Sequences by species
> 2) Grab the DN/DS for various branch points from Pig to Human
> If I need to I will grab the gene ID for each species and then determine the proper nucleotide sequence and grab those, using the newick calculate Dn/DS using PAML to get descendant predicted LCA sequences.
> Is there a better way to do this than I have outlined?
> Joe
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